Build #1

Build: #1 was successful

Job: Clover and Tests was successful

Stages & jobs

  1. Default Stage

Build log

The build generated 315 lines of output. Download or view full build log

16-Jun-2026 16:23:14 Build Jalview Builds - Gradle Develop Build - patch-JAL-3848_slivka_java_client_update_06d3659 - Clover and Tests #1 (JB-GDB755-JOB1-1) started building on agent Default Agent
16-Jun-2026 16:23:14
16-Jun-2026 16:23:14 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1
16-Jun-2026 16:23:14 Executing build Jalview Builds - Gradle Develop Build - patch-JAL-3848_slivka_java_client_update_06d3659 - Clover and Tests #1 (JB-GDB755-JOB1-1)
16-Jun-2026 16:23:14 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
16-Jun-2026 16:23:14 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1
16-Jun-2026 16:23:14 Updating source code to revision: 261c20c53e615aa27321e6aa6e75bfedf4e50e9f
16-Jun-2026 16:23:14 Fetching 'refs/heads/patch/JAL-3848_slivka_java_client_update_06d3659' from 'https://gitlab.jalview.org/jalview/jalview.git'.
16-Jun-2026 16:23:14 Checking out revision 261c20c53e615aa27321e6aa6e75bfedf4e50e9f.
16-Jun-2026 16:23:14 Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1/.git'.
16-Jun-2026 16:23:14 Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1'...
16-Jun-2026 16:23:14 done.
16-Jun-2026 16:23:21 Branch patch/JAL-3848_slivka_java_client_update_06d3659 set up to track remote branch patch/JAL-3848_slivka_java_client_update_06d3659 from origin.
16-Jun-2026 16:23:21 Switched to a new branch 'patch/JAL-3848_slivka_java_client_update_06d3659'
16-Jun-2026 16:23:21 Updated source code to revision: 261c20c53e615aa27321e6aa6e75bfedf4e50e9f
16-Jun-2026 16:23:21 Finished task 'Checkout Default Repository' with result: Success
16-Jun-2026 16:23:21 Running pre-build action: VCS Version Collector
16-Jun-2026 16:23:21 Running pre-build action: Artifactory Release Staging
16-Jun-2026 16:23:21 Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
16-Jun-2026 16:23:21 Bamboo Artifactory Plugin version: 2.6.2
16-Jun-2026 16:23:21
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-3848_slivka_java_client_update_06d3659 - Clover and Tests #1 (JB-GDB755-JOB1-1)'
... 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-GDB755-JOB1
... using extra environment variables:
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bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB755-JOB1-1
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16-Jun-2026 16:23:21 2414
16-Jun-2026 16:23:21 Starting a Gradle Daemon (subsequent builds will be faster)
16-Jun-2026 16:23:30
16-Jun-2026 16:23:30 > Configure project :
16-Jun-2026 16:23:30 Using properties from file './utils/channels/default/channel_gradle.properties'
16-Jun-2026 16:23:30 JALVIEW_VERSION is set to '2.12.0'
16-Jun-2026 16:23:30 HEADLESS BUILD
16-Jun-2026 16:23:30 J2S ENABLED
16-Jun-2026 16:23:30 Using a LOCAL profile.
16-Jun-2026 16:23:31 eclipseDir exists
16-Jun-2026 16:23:31
16-Jun-2026 16:23:31 > Task :clean
16-Jun-2026 16:23:31 > Task :cleanClover
16-Jun-2026 16:23:31 > Task :cleanTest UP-TO-DATE
16-Jun-2026 16:23:34
16-Jun-2026 16:23:34 > Task :cloverInstrJava
16-Jun-2026 16:23:34 Clover: About to instrument 1253 files
16-Jun-2026 16:23:34 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
16-Jun-2026 16:23:34 Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1/build/clover/clover.db'.
16-Jun-2026 16:23:34 Processing files at 1.9 source level.
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:38 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?
16-Jun-2026 16:23:43 Clover all over. Instrumented 1253 files (133 packages).
16-Jun-2026 16:23:46
16-Jun-2026 16:23:46 > Task :cloverInstrTests
16-Jun-2026 16:23:46 Clover: About to instrument test files
16-Jun-2026 16:23:46 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
16-Jun-2026 16:23:46 Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1/build/clover/clover.db'.
16-Jun-2026 16:23:46 Processing files at 1.9 source level.
16-Jun-2026 16:23:48 Clover all over. Instrumented 315 files (58 packages).
16-Jun-2026 16:23:48 1770 test methods detected.
16-Jun-2026 16:23:48
16-Jun-2026 16:23:48 > Task :cloverInstr
16-Jun-2026 16:23:52
16-Jun-2026 16:23:52 > Task :compileCloverJava
16-Jun-2026 16:23:52 Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons:
16-Jun-2026 16:23:52   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-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.
16-Jun-2026 16:23:52   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-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.
16-Jun-2026 16:23:52   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-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.
16-Jun-2026 16:23:52 Setting target compatibility to 11
16-Jun-2026 16:24:15 Note: Some input files use or override a deprecated API.
16-Jun-2026 16:24:15 Note: Recompile with -Xlint:deprecation for details.
16-Jun-2026 16:24:15 Note: Some input files use unchecked or unsafe operations.
16-Jun-2026 16:24:15 Note: Recompile with -Xlint:unchecked for details.
16-Jun-2026 16:24:22
16-Jun-2026 16:24:22 > Task :processCloverResources NO-SOURCE
16-Jun-2026 16:24:22 > Task :cloverClasses
16-Jun-2026 16:24:22 > Task :copyHelp
16-Jun-2026 16:24:23 > Task :buildIndices
16-Jun-2026 16:24:23 > Task :copyResources
16-Jun-2026 16:24:23 > Task :copyChannelResources
16-Jun-2026 16:24:23
16-Jun-2026 16:24:23 > Task :createBuildProperties
16-Jun-2026 16:24:23 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
16-Jun-2026 16:24:23   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-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.
16-Jun-2026 16:24:23
16-Jun-2026 16:24:23 > Task :buildResources
16-Jun-2026 16:24:23 > Task :copyDocs
16-Jun-2026 16:24:24
16-Jun-2026 16:24:24 > Task :convertMdFiles
16-Jun-2026 16:24:24 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
16-Jun-2026 16:24:24 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1/build/resources/doc_build/doc/releaseprocess.html
16-Jun-2026 16:24:24 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
16-Jun-2026 16:24:24 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1/build/resources/doc_build/doc/JalviewJS-API.html
16-Jun-2026 16:24:24 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1/build/resources/doc_build/doc/building.html
16-Jun-2026 16:24:24 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1/build/resources/doc_build/doc/addingWebClient.html
16-Jun-2026 16:24:24 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1/build/resources/doc_build/doc/jalview-projects.html
16-Jun-2026 16:24:24 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html
16-Jun-2026 16:24:24
16-Jun-2026 16:24:24 > Task :releasesTemplates
16-Jun-2026 16:24:24 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
16-Jun-2026 16:24:24   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-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.
16-Jun-2026 16:24:24   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-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.
16-Jun-2026 16:24:24 Stripping rc/test/etc for TEST
16-Jun-2026 16:24:24 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1/help/markdown/whatsnew/whatsnew-TEST.md
16-Jun-2026 16:24:24
16-Jun-2026 16:24:24 > Task :prepare
16-Jun-2026 16:24:26
16-Jun-2026 16:24:26 > Task :compileJava
16-Jun-2026 16:24:26 Setting target compatibility to 11
16-Jun-2026 16:24:32 Note: Some input files use or override a deprecated API.
16-Jun-2026 16:24:32 Note: Recompile with -Xlint:deprecation for details.
16-Jun-2026 16:24:32 Note: Some input files use unchecked or unsafe operations.
16-Jun-2026 16:24:32 Note: Recompile with -Xlint:unchecked for details.
16-Jun-2026 16:24:37
16-Jun-2026 16:24:37 > Task :compileTestJava
16-Jun-2026 16:24:37 Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons:
16-Jun-2026 16:24:37   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-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.
16-Jun-2026 16:24:37   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-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.
16-Jun-2026 16:24:37 Setting target compatibility to 11
16-Jun-2026 16:24:42 Note: Some input files use or override a deprecated API.
16-Jun-2026 16:24:42 Note: Recompile with -Xlint:deprecation for details.
16-Jun-2026 16:24:42 Note: Some input files use unchecked or unsafe operations.
16-Jun-2026 16:24:42 Note: Recompile with -Xlint:unchecked for details.
16-Jun-2026 16:24:43
16-Jun-2026 16:24:43 > Task :processTestResources
16-Jun-2026 16:24:43 Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons:
16-Jun-2026 16:24:43   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-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.
16-Jun-2026 16:24:43   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-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.
16-Jun-2026 16:24:43   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-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.
16-Jun-2026 16:24:43   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-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.
16-Jun-2026 16:24:43   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-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.
16-Jun-2026 16:24:43   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-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.
16-Jun-2026 16:24:43   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-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.
16-Jun-2026 16:24:43
16-Jun-2026 16:24:43 > Task :testClasses
16-Jun-2026 16:24:45
16-Jun-2026 16:24:45 > Task :testTask0
16-Jun-2026 16:24:45 Running tests WITH clover
16-Jun-2026 16:24:46 WARNING: An illegal reflective access operation has occurred
16-Jun-2026 16:24:46 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
16-Jun-2026 16:24:46 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
16-Jun-2026 16:24:46 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
16-Jun-2026 16:24:46 WARNING: All illegal access operations will be denied in a future release
16-Jun-2026 16:27:07 [143.314s][warning][gc,alloc] AWT-EventQueue-0: Retried waiting for GCLocker too often allocating 135080516 words
16-Jun-2026 16:29:12
16-Jun-2026 16:29:12 > Task :testTask1
16-Jun-2026 16:29:12 Running tests WITH clover
16-Jun-2026 16:29:13 WARNING: An illegal reflective access operation has occurred
16-Jun-2026 16:29:13 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
16-Jun-2026 16:29:13 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
16-Jun-2026 16:29:13 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
16-Jun-2026 16:29:13 WARNING: All illegal access operations will be denied in a future release
16-Jun-2026 16:31:18
16-Jun-2026 16:31:18 > Task :testTask2
16-Jun-2026 16:31:18 Running tests WITH clover
16-Jun-2026 16:31:19 WARNING: An illegal reflective access operation has occurred
16-Jun-2026 16:31:19 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
16-Jun-2026 16:31:19 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
16-Jun-2026 16:31:19 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
16-Jun-2026 16:31:19 WARNING: All illegal access operations will be denied in a future release
16-Jun-2026 16:31:23
16-Jun-2026 16:31:23 > Task :testTask3
16-Jun-2026 16:31:23 Running tests WITH clover
16-Jun-2026 16:31:24 WARNING: An illegal reflective access operation has occurred
16-Jun-2026 16:31:24 WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName
16-Jun-2026 16:31:24 WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
16-Jun-2026 16:31:24 WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
16-Jun-2026 16:31:24 WARNING: All illegal access operations will be denied in a future release
16-Jun-2026 16:31:42
16-Jun-2026 16:31:42 > Task :test NO-SOURCE
16-Jun-2026 16:31:42 ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
16-Jun-2026 16:31:42 │jalview:testTask0 results: SUCCESS (2103 tests, 2103 successes, 0 failures, 0 skipped) in 4 minutes, 25.602 seconds   │
16-Jun-2026 16:31:42 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1/build/reports/tests/testTask0/index.html│
16-Jun-2026 16:31:42 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
16-Jun-2026 16:31:42 │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 6.557 seconds        │
16-Jun-2026 16:31:42 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1/build/reports/tests/testTask1/index.html│
16-Jun-2026 16:31:42 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
16-Jun-2026 16:31:42 │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.752 seconds                     │
16-Jun-2026 16:31:42 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1/build/reports/tests/testTask2/index.html│
16-Jun-2026 16:31:42 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
16-Jun-2026 16:31:42 │jalview:testTask3 results: SUCCESS (14 tests, 13 successes, 0 failures, 1 skipped) in 20.539 seconds                  │
16-Jun-2026 16:31:42 │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1/build/reports/tests/testTask3/index.html│
16-Jun-2026 16:31:42 ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
16-Jun-2026 16:31:42 │OVERALL: results: SUCCESS (2180 tests, 2179 successes, 0 failures, 1 skipped) in 6 minutes, 57.450 seconds            │
16-Jun-2026 16:31:42 └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
16-Jun-2026 16:31:42
16-Jun-2026 16:31:42 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
16-Jun-2026 16:31:42
16-Jun-2026 16:31:42 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
16-Jun-2026 16:31:42
16-Jun-2026 16:31:42 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
16-Jun-2026 16:31:42
16-Jun-2026 16:31:42 Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness.
16-Jun-2026 16:31:42 Please consult deprecation warnings for more details.
16-Jun-2026 16:31:42
16-Jun-2026 16:31:42 BUILD SUCCESSFUL in 8m 21s
16-Jun-2026 16:31:42 21 actionable tasks: 20 executed, 1 up-to-date
16-Jun-2026 16:31:42 Finished task 'Run tests with openclover under gradle' with result: Success
16-Jun-2026 16:31:42 Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
16-Jun-2026 16:31:42 Bamboo Artifactory Plugin version: 2.6.2
16-Jun-2026 16:31:42
Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - patch-JAL-3848_slivka_java_client_update_06d3659 - Clover and Tests #1 (JB-GDB755-JOB1-1)'
... 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-GDB755-JOB1
... using extra environment variables:
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CATALINA_PID=/home/bamboo/latest/work/bamboo.pid
bamboo_planRepository_1_branchDisplayName=patch/JAL-3848_slivka_java_client_update_06d3659
bamboo_repository_revision_number=261c20c53e615aa27321e6aa6e75bfedf4e50e9f
bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB755-JOB1-1
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-GDB755-JOB1
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SHELL=/bin/bash
bamboo_repository_48169076_name=Jalview Gitlab
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bamboo_planName=Jalview Builds - Gradle Develop Build - patch-JAL-3848_slivka_java_client_update_06d3659
bamboo_shortPlanKey=GDB755
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bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk
bamboo_planRepository_revision=261c20c53e615aa27321e6aa6e75bfedf4e50e9f
bamboo_buildTimeStamp=2026-06-16T16:23:14.455+01:00
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bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11
bamboo_planRepository_1_revision=261c20c53e615aa27321e6aa6e75bfedf4e50e9f
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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/
bamboo_repository_48169076_branch_name=patch/JAL-3848_slivka_java_client_update_06d3659
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bamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle
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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
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bamboo_tmp_directory=/srv/bamboo/bamboo-home/temp
bamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1
bamboo_planKey=JB-GDB755
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bamboo_planRepository_username=
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16-Jun-2026 16:31:42 2414
16-Jun-2026 16:31:48
16-Jun-2026 16:31:48 > Configure project :
16-Jun-2026 16:31:48 Using properties from file './utils/channels/default/channel_gradle.properties'
16-Jun-2026 16:31:48 JALVIEW_VERSION is set to '2.12.0'
16-Jun-2026 16:31:48 HEADLESS BUILD
16-Jun-2026 16:31:48 J2S ENABLED
16-Jun-2026 16:31:48 Using a LOCAL profile.
16-Jun-2026 16:31:49 eclipseDir exists
16-Jun-2026 16:31:51
16-Jun-2026 16:31:51 > Task :cloverHtmlReport
16-Jun-2026 16:31:51 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
16-Jun-2026 16:31:53 Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1/build/reports/clover'
16-Jun-2026 16:32:45 Done. Processed 137 packages in 52782ms (385ms per package).
16-Jun-2026 16:32:51
16-Jun-2026 16:32:51 > Task :cloverXmlReport
16-Jun-2026 16:32:51 OpenClover Version 4.4.1, built on October 11 2019 (build-1020)
16-Jun-2026 16:32:52 Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1/build/reports/clover/clover.xml'
16-Jun-2026 16:32:52
16-Jun-2026 16:32:52 > Task :cloverReport
16-Jun-2026 16:32:52
16-Jun-2026 16:32:52 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
16-Jun-2026 16:32:52
16-Jun-2026 16:32:52 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
16-Jun-2026 16:32:52
16-Jun-2026 16:32:52 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
16-Jun-2026 16:32:52
16-Jun-2026 16:32:52 BUILD SUCCESSFUL in 1m 10s
16-Jun-2026 16:32:52 2 actionable tasks: 2 executed
16-Jun-2026 16:32:53 Finished task 'Clover Report' with result: Success
16-Jun-2026 16:32:53 Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
16-Jun-2026 16:32:53 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1...
16-Jun-2026 16:32:53 Finished task 'TestNG Parser' with result: Success
16-Jun-2026 16:32:53 Running post build plugin 'NCover Results Collector'
16-Jun-2026 16:32:53 Running post build plugin 'Artifact Copier'
16-Jun-2026 16:32:53 Publishing an artifact: Clover Report (System)
16-Jun-2026 16:32:55 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.980 s
16-Jun-2026 16:32:55 Publishing an artifact: TestNG report
16-Jun-2026 16:32:55 Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB755-JOB1/build/reports/tests/test does not exist.
16-Jun-2026 16:32:55 The artifact hasn't been successfully published after 3.964 ms
16-Jun-2026 16:32:55 Running post build plugin 'Artifactory Release Management Staging'
16-Jun-2026 16:32:55 Running post build plugin 'Artifactory Build Info Copier'
16-Jun-2026 16:32:55 Running post build plugin 'Artifactory Gradle Properties Info Copier'
16-Jun-2026 16:32:55 Running post build plugin 'npm Cache Cleanup'
16-Jun-2026 16:32:55 Running post build plugin 'Clover Results Collector'
16-Jun-2026 16:32:55 Running post build plugin 'Docker Container Cleanup'
16-Jun-2026 16:32:55 Finalising the build...
16-Jun-2026 16:32:55 Stopping timer.
16-Jun-2026 16:32:55 Build JB-GDB755-JOB1-1 completed.
16-Jun-2026 16:32:55 Running on server: post build plugin 'NCover Results Collector'
16-Jun-2026 16:32:55 Running on server: post build plugin 'Build Hanging Detection Configuration'
16-Jun-2026 16:32:55 Running on server: post build plugin 'Clover Delta Calculator'
16-Jun-2026 16:32:55 Running on server: post build plugin 'Maven Dependencies Postprocessor'
16-Jun-2026 16:32:55 All post build plugins have finished
16-Jun-2026 16:32:55 Generating build results summary...
16-Jun-2026 16:32:55 Saving build results to disk...
16-Jun-2026 16:32:55 Logging substituted variables...
16-Jun-2026 16:32:55 Indexing build results...
16-Jun-2026 16:32:55 Finished building JB-GDB755-JOB1-1.