Build #2

Build: #2 was successful

Job: Default Job was successful

Stages & jobs

  1. Default Stage

Build log

The build generated 192 lines of output. Download or view full build log

07-Nov-2024 13:14:37 Build Jalview Builds - Getdown DEVELOP Launchers - experiment-JAL-4386_experimental_string_to_colour_scheme_methods - Default Job #2 (JB-GDL38-JOB1-2) started building on agent Default Agent
07-Nov-2024 13:14:37
07-Nov-2024 13:14:37 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1
07-Nov-2024 13:14:37 Executing build Jalview Builds - Getdown DEVELOP Launchers - experiment-JAL-4386_experimental_string_to_colour_scheme_methods - Default Job #2 (JB-GDL38-JOB1-2)
07-Nov-2024 13:14:37 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
07-Nov-2024 13:14:37 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1
07-Nov-2024 13:14:37 Updating source code to revision: cfb973824e06936f2f3b2c4cf9605bd687896cf4
07-Nov-2024 13:14:37 Fetching 'refs/heads/experiment/JAL-4386_experimental_string_to_colour_scheme_methods' from 'http://source.jalview.org/git/jalview.git'.
07-Nov-2024 13:14:38 Checking out revision cfb973824e06936f2f3b2c4cf9605bd687896cf4.
07-Nov-2024 13:14:38 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164
07-Nov-2024 13:14:38    503c832..cfb9738  experiment/JAL-4386_experimental_string_to_colour_scheme_methods -> origin/experiment/JAL-4386_experimental_string_to_colour_scheme_methods
07-Nov-2024 13:14:38    e1ff67b..1c79fdc  feature/JAL-4386_JAL-4435_reformat_node_labels -> origin/feature/JAL-4386_JAL-4435_reformat_node_labels
07-Nov-2024 13:14:40 Already on 'experiment/JAL-4386_experimental_string_to_colour_scheme_methods'
07-Nov-2024 13:14:40 Your branch is behind 'origin/experiment/JAL-4386_experimental_string_to_colour_scheme_methods' by 4 commits, and can be fast-forwarded.
07-Nov-2024 13:14:40   (use "git pull" to update your local branch)
07-Nov-2024 13:14:40 HEAD is now at cfb9738 JAL-4386 Fixed to the colour scheme ranges and application to the normal calculated tree
07-Nov-2024 13:14:40 Updated source code to revision: cfb973824e06936f2f3b2c4cf9605bd687896cf4
07-Nov-2024 13:14:40 Finished task 'Checkout Default Repository' with result: Success
07-Nov-2024 13:14:40 Running pre-build action: VCS Version Collector
07-Nov-2024 13:14:40 Running pre-build action: Artifactory Release Staging
07-Nov-2024 13:14:40
Substituting variable: ${bamboo.planKey} with JB-GDL38
07-Nov-2024 13:14:40 Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
07-Nov-2024 13:14:40 Bamboo Artifactory Plugin version: 2.6.2
07-Nov-2024 13:14:40
Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - experiment-JAL-4386_experimental_string_to_colour_scheme_methods - Default Job #2 (JB-GDL38-JOB1-2)'
... running command line:
/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL38 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown
... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1
... using extra environment variables:
bamboo_planRepository_1_branch=experiment/JAL-4386_experimental_string_to_colour_scheme_methods
bamboo_dependency_parent_0=JB-GDB640-2
bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr
CATALINA_PID=/home/bamboo/latest/work/bamboo.pid
bamboo_dependency_parent_total=1
bamboo_planRepository_1_branchDisplayName=experiment/JAL-4386_experimental_string_to_colour_scheme_methods
bamboo_repository_revision_number=cfb973824e06936f2f3b2c4cf9605bd687896cf4
bamboo_repository_46498175_revision_number=cfb973824e06936f2f3b2c4cf9605bd687896cf4
bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL38-JOB1-2
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-GDL38-JOB1
bamboo_planRepository_1_name=Jalview Git
bamboo_buildKey=JB-GDL38-JOB1
bamboo_shortPlanName=experiment-JAL-4386_experimental_string_to_colour_scheme_methods
bamboo_planRepository_name=Jalview Git
LOGNAME=bamboo
bamboo_buildNumber=2
PWD=/
bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse
bamboo_shortJobName=Default Job
bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDL38-JOB1-2
bamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git
SHELL=/bin/bash
bamboo_agentId=196609
bamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - experiment-JAL-4386_experimental_string_to_colour_scheme_methods
bamboo_shortPlanKey=GDL38
bamboo_shortJobKey=JOB1
bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk
bamboo_planRepository_revision=cfb973824e06936f2f3b2c4cf9605bd687896cf4
bamboo_buildTimeStamp=2024-11-07T13:09:27.703Z
bamboo_repository_previous_revision_number=503c83212e9779b412c999dc1d64d4e6c5e41cae
bamboo_repository_git_branch=experiment/JAL-4386_experimental_string_to_colour_scheme_methods
bamboo_buildResultKey=JB-GDL38-JOB1-2
bamboo_repository_branch_name=experiment/JAL-4386_experimental_string_to_colour_scheme_methods
bamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - experiment-JAL-4386_experimental_string_to_colour_scheme_methods - Default Job
bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11
bamboo_planRepository_1_revision=cfb973824e06936f2f3b2c4cf9605bd687896cf4
SHLVL=1
bamboo_CHANNEL=DEVELOP
bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant
bamboo_repository_46498175_git_repositoryUrl=http://source.jalview.org/git/jalview.git
bamboo_repository_name=Jalview Git
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_repository_46498175_name=Jalview Git
bamboo_planRepository_branch=experiment/JAL-4386_experimental_string_to_colour_scheme_methods
bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609
bamboo_repository_46498175_git_branch=experiment/JAL-4386_experimental_string_to_colour_scheme_methods
bamboo_capability_system_git_executable=/bin/git
bamboo_repository_git_username=
bamboo_planRepository_branchDisplayName=experiment/JAL-4386_experimental_string_to_colour_scheme_methods
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bamboo_planRepository_branchName=experiment/JAL-4386_experimental_string_to_colour_scheme_methods
_=/usr/bin/java
bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11
bamboo_capability_system_builderivy_Ivy=/usr
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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_repository_46498175_branch_name=experiment/JAL-4386_experimental_string_to_colour_scheme_methods
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_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-GDL38-JOB1
bamboo_planKey=JB-GDL38
bamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git
bamboo_planRepository_username=
bamboo_repository_46498175_previous_revision_number=503c83212e9779b412c999dc1d64d4e6c5e41cae
bamboo_repository_46498175_git_username=
HOME=/home/bamboo
bamboo_planRepository_1_branchName=experiment/JAL-4386_experimental_string_to_colour_scheme_methods
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07-Nov-2024 13:14:41
07-Nov-2024 13:14:41 > Configure project :
07-Nov-2024 13:14:41 Using properties from file './utils/channels/default/channel_gradle.properties'
07-Nov-2024 13:14:41 JALVIEW_VERSION is set to '2.11.4.1'
07-Nov-2024 13:14:41 HEADLESS BUILD
07-Nov-2024 13:14:41 J2S ENABLED
07-Nov-2024 13:14:41 Using a BUILD profile.
07-Nov-2024 13:14:41 eclipseDir exists
07-Nov-2024 13:14:41
07-Nov-2024 13:14:41 > Task :clean
07-Nov-2024 13:14:41 > Task :cleanPackageDir
07-Nov-2024 13:14:41 > Task :getdownImagesCopy
07-Nov-2024 13:14:41 > Task :getdownImagesProcess
07-Nov-2024 13:14:41 > Task :getdownImages
07-Nov-2024 13:14:42 > Task :copyHelp
07-Nov-2024 13:14:43 > Task :buildIndices
07-Nov-2024 13:14:43 > Task :copyResources
07-Nov-2024 13:14:43 > Task :copyChannelResources
07-Nov-2024 13:14:43
07-Nov-2024 13:14:43 > Task :createBuildProperties
07-Nov-2024 13:14:43 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
07-Nov-2024 13:14:43   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-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.
07-Nov-2024 13:14:43
07-Nov-2024 13:14:43 > Task :buildResources
07-Nov-2024 13:14:43 > Task :copyDocs
07-Nov-2024 13:14:43
07-Nov-2024 13:14:43 > Task :convertMdFiles
07-Nov-2024 13:14:43 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
07-Nov-2024 13:14:43 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1/build/resources/doc_build/doc/releaseprocess.html
07-Nov-2024 13:14:43 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
07-Nov-2024 13:14:43 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1/build/resources/doc_build/doc/building.html
07-Nov-2024 13:14:43 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1/build/resources/doc_build/doc/jalview-projects.html
07-Nov-2024 13:14:43
07-Nov-2024 13:14:43 > Task :releasesTemplates
07-Nov-2024 13:14:43 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
07-Nov-2024 13:14:43   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-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.
07-Nov-2024 13:14:43   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-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.
07-Nov-2024 13:14:43 Stripping rc/test/etc for 2_11_4_1
07-Nov-2024 13:14:43 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1/help/markdown/whatsnew/whatsnew-2_11_4_1.md
07-Nov-2024 13:14:43
07-Nov-2024 13:14:43 > Task :prepare
07-Nov-2024 13:14:45
07-Nov-2024 13:14:45 > Task :compileJava
07-Nov-2024 13:14:45 Setting target compatibility to 11
07-Nov-2024 13:14:51 Note: Some input files use or override a deprecated API.
07-Nov-2024 13:14:51 Note: Recompile with -Xlint:deprecation for details.
07-Nov-2024 13:14:51 Note: Some input files use unchecked or unsafe operations.
07-Nov-2024 13:14:51 Note: Recompile with -Xlint:unchecked for details.
07-Nov-2024 13:14:51
07-Nov-2024 13:14:51 > Task :processResources
07-Nov-2024 13:14:51 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
07-Nov-2024 13:14:51   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1/build/resources/doc_build'. Reason: Task ':processResources' uses this output of task ':convertMdFiles' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
07-Nov-2024 13:14:51   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1/build/resources/doc_build'. Reason: Task ':processResources' uses this output of task ':copyDocs' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
07-Nov-2024 13:14:51   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':buildIndices' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
07-Nov-2024 13:14:51   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':copyHelp' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
07-Nov-2024 13:14:51   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
07-Nov-2024 13:14:51   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
07-Nov-2024 13:14:51   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':copyResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
07-Nov-2024 13:14:51   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':createBuildProperties' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
07-Nov-2024 13:14:51
07-Nov-2024 13:14:51 > Task :classes
07-Nov-2024 13:14:53
07-Nov-2024 13:14:53 > Task :compileLinkCheck
07-Nov-2024 13:14:53 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
07-Nov-2024 13:14:53   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1/utils'. Reason: Task ':convertMdFiles' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
07-Nov-2024 13:14:53   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1/utils'. Reason: Task ':copyChannelResources' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
07-Nov-2024 13:14:53   - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1/utils'. Reason: Task ':getdownImagesCopy' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem.
07-Nov-2024 13:14:55
07-Nov-2024 13:14:55 > Task :linkCheck
07-Nov-2024 13:14:55 Checking help file links
07-Nov-2024 13:17:00
07-Nov-2024 13:17:00 Results:
07-Nov-2024 13:17:00 159 distinct help targets
07-Nov-2024 13:17:00 159 help mappings
07-Nov-2024 13:17:00 0 invalid targets
07-Nov-2024 13:17:00 32 unused targets
07-Nov-2024 13:17:00     uniprotfetcher: html/features/uniprotsequencefetcher.html
07-Nov-2024 13:17:00     overviewprefs: html/features/preferences.html#overview
07-Nov-2024 13:17:00     cdnafeatures: html/features/codingfeatures.html
07-Nov-2024 13:17:00     startupprefs: html/features/preferences.html#startup
07-Nov-2024 13:17:00     ensemblfetch: html/features/ensemblsequencefetcher.html
07-Nov-2024 13:17:00     io.modellerpir: html/io/modellerpir.html
07-Nov-2024 13:17:00     structureandpaefromfile: html/features/structurechooser.html#loadfromfile
07-Nov-2024 13:17:00     pdbmcviewer: html/features/pdbviewer.html
07-Nov-2024 13:17:00     workingwithpae: html/features/paematrices.html
07-Nov-2024 13:17:00     groovy.colours: html/features/groovy.html#groovyColours
07-Nov-2024 13:17:00     seqmappings: html/features/seqmappings.html
07-Nov-2024 13:17:00     uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
07-Nov-2024 13:17:00     splitframe.mirrorfonts: html/features/splitView.html#mirror
07-Nov-2024 13:17:00     subtMatrices.pam250: html/calculations/scorematrices.html#pam250
07-Nov-2024 13:17:00     search: html/features/search.html
07-Nov-2024 13:17:00     viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
07-Nov-2024 13:17:00     alformats: html/io/fileformats.html
07-Nov-2024 13:17:00     strucprefs: html/features/preferences.html#structure
07-Nov-2024 13:17:00     siftsmapping: html/features/siftsmapping.html
07-Nov-2024 13:17:00     chimera.annotxfer: html/features/chimera.html#annotxfer
07-Nov-2024 13:17:00     pdbfts: html/features/pdbsequencefetcher.html#pdbfts
07-Nov-2024 13:17:00     newkeys: html/features/newkeystrokes.html
07-Nov-2024 13:17:00     importvcf.attribs: html/features/importvcf.html#attribs
07-Nov-2024 13:17:00     seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
07-Nov-2024 13:17:00     structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
07-Nov-2024 13:17:00     jalarchive: html/features/jalarchive.html
07-Nov-2024 13:17:00     newsreader: html/webServices/newsreader.html
07-Nov-2024 13:17:00     jalviewcltool: html/features/commandline.html#script
07-Nov-2024 13:17:00     popMenuAddref: html/menus/popupMenu.html#addrefannot
07-Nov-2024 13:17:00     splitframe.virtualfeats: html/features/splitView.html#virtualfeats
07-Nov-2024 13:17:00     paematrixformat: html/io/paematrixformat.html
07-Nov-2024 13:17:00     overview: html/features/overview.html
07-Nov-2024 13:17:00 0 invalid map urls
07-Nov-2024 13:17:00 0 invalid image attributes
07-Nov-2024 13:17:00 508 internal href links (110 with anchors)
07-Nov-2024 13:17:00 0 invalid internal href links
07-Nov-2024 13:17:00 0 invalid internal anchor links
07-Nov-2024 13:17:00 113 external href links
07-Nov-2024 13:17:00 External links not verified as internet not available
07-Nov-2024 13:17:00 *** Success ***
07-Nov-2024 13:17:01
07-Nov-2024 13:17:01 > Task :jar
07-Nov-2024 13:17:01 > Task :syncJars
07-Nov-2024 13:17:01 > Task :makeDist
07-Nov-2024 13:17:02 > Task :getdownWebsiteBuild
07-Nov-2024 13:17:03 2024/11/07 13:17:02:500 WARNING Starting without install4j classes
07-Nov-2024 13:17:03 2024/11/07 13:17:03:063 WARNING Starting without install4j classes
07-Nov-2024 13:17:03
07-Nov-2024 13:17:03 > Task :getdownDigest
07-Nov-2024 13:17:03 Generating digest file './build/website/docroot/getdown/default/11/digest.txt'...
07-Nov-2024 13:17:03 Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'...
07-Nov-2024 13:17:03
07-Nov-2024 13:17:03 > Task :getdown
07-Nov-2024 13:17:03
07-Nov-2024 13:17:03 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
07-Nov-2024 13:17:03
07-Nov-2024 13:17:03 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
07-Nov-2024 13:17:03
07-Nov-2024 13:17:03 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
07-Nov-2024 13:17:03
07-Nov-2024 13:17:03 Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness.
07-Nov-2024 13:17:03 Please consult deprecation warnings for more details.
07-Nov-2024 13:17:03
07-Nov-2024 13:17:03 BUILD SUCCESSFUL in 2m 23s
07-Nov-2024 13:17:03 21 actionable tasks: 21 executed
07-Nov-2024 13:17:04 Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success
07-Nov-2024 13:17:04 Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
07-Nov-2024 13:17:04
Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - experiment-JAL-4386_experimental_string_to_colour_scheme_methods - Default Job #2 (JB-GDL38-JOB1-2)'
... running command line:
/srv/bamboo/bamboo-home/temp/JB-GDL38-JOB1-2-ScriptBuildTask-3531866373606566889.sh
... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1
... using extra environment variables:
bamboo_planRepository_1_branch=experiment/JAL-4386_experimental_string_to_colour_scheme_methods
bamboo_dependency_parent_0=JB-GDB640-2
bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr
bamboo_dependency_parent_total=1
bamboo_planRepository_1_branchDisplayName=experiment/JAL-4386_experimental_string_to_colour_scheme_methods
bamboo_repository_revision_number=cfb973824e06936f2f3b2c4cf9605bd687896cf4
bamboo_repository_46498175_revision_number=cfb973824e06936f2f3b2c4cf9605bd687896cf4
bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL38-JOB1-2
bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL38-JOB1
bamboo_planRepository_1_name=Jalview Git
bamboo_buildKey=JB-GDL38-JOB1
bamboo_shortPlanName=experiment-JAL-4386_experimental_string_to_colour_scheme_methods
bamboo_planRepository_name=Jalview Git
bamboo_buildNumber=2
bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse
bamboo_shortJobName=Default Job
bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDL38-JOB1-2
bamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git
bamboo_agentId=196609
bamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - experiment-JAL-4386_experimental_string_to_colour_scheme_methods
bamboo_shortPlanKey=GDL38
bamboo_shortJobKey=JOB1
bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk
bamboo_planRepository_revision=cfb973824e06936f2f3b2c4cf9605bd687896cf4
bamboo_buildTimeStamp=2024-11-07T13:09:27.703Z
bamboo_repository_previous_revision_number=503c83212e9779b412c999dc1d64d4e6c5e41cae
bamboo_repository_git_branch=experiment/JAL-4386_experimental_string_to_colour_scheme_methods
bamboo_buildResultKey=JB-GDL38-JOB1-2
bamboo_repository_branch_name=experiment/JAL-4386_experimental_string_to_colour_scheme_methods
bamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - experiment-JAL-4386_experimental_string_to_colour_scheme_methods - Default Job
bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11
bamboo_planRepository_1_revision=cfb973824e06936f2f3b2c4cf9605bd687896cf4
bamboo_CHANNEL=DEVELOP
bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant
bamboo_repository_46498175_git_repositoryUrl=http://source.jalview.org/git/jalview.git
bamboo_repository_name=Jalview Git
bamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL38 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown
bamboo_buildFailed=false
bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk
bamboo_repository_46498175_name=Jalview Git
bamboo_planRepository_branch=experiment/JAL-4386_experimental_string_to_colour_scheme_methods
bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609
bamboo_repository_46498175_git_branch=experiment/JAL-4386_experimental_string_to_colour_scheme_methods
bamboo_capability_system_git_executable=/bin/git
bamboo_repository_git_username=
bamboo_planRepository_branchDisplayName=experiment/JAL-4386_experimental_string_to_colour_scheme_methods
bamboo_planRepository_1_type=gitv2
bamboo_planRepository_branchName=experiment/JAL-4386_experimental_string_to_colour_scheme_methods
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-46301949
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_repository_46498175_branch_name=experiment/JAL-4386_experimental_string_to_colour_scheme_methods
bamboo_planRepository_type=gitv2
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_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-GDL38-JOB1
bamboo_planKey=JB-GDL38
bamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git
bamboo_planRepository_username=
bamboo_repository_46498175_previous_revision_number=503c83212e9779b412c999dc1d64d4e6c5e41cae
bamboo_repository_46498175_git_username=
bamboo_planRepository_1_branchName=experiment/JAL-4386_experimental_string_to_colour_scheme_methods
07-Nov-2024 13:17:04 Finished task 'Copy JVL file and produce link in HTML' with result: Success
07-Nov-2024 13:17:04 Running post build plugin 'NCover Results Collector'
07-Nov-2024 13:17:04 Running post build plugin 'Artifact Copier'
07-Nov-2024 13:17:04 Publishing an artifact: getdown
07-Nov-2024 13:17:04 Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 98.74 ms
07-Nov-2024 13:17:04 Running post build plugin 'Artifactory Release Management Staging'
07-Nov-2024 13:17:04 Running post build plugin 'Artifactory Build Info Copier'
07-Nov-2024 13:17:04 Running post build plugin 'Artifactory Gradle Properties Info Copier'
07-Nov-2024 13:17:04 Running post build plugin 'npm Cache Cleanup'
07-Nov-2024 13:17:04 Running post build plugin 'Clover Results Collector'
07-Nov-2024 13:17:04 Running post build plugin 'Docker Container Cleanup'
07-Nov-2024 13:17:04 Finalising the build...
07-Nov-2024 13:17:04 Stopping timer.
07-Nov-2024 13:17:04 Build JB-GDL38-JOB1-2 completed.
07-Nov-2024 13:17:04 Running on server: post build plugin 'NCover Results Collector'
07-Nov-2024 13:17:04 Running on server: post build plugin 'Build Hanging Detection Configuration'
07-Nov-2024 13:17:04 Running on server: post build plugin 'Clover Delta Calculator'
07-Nov-2024 13:17:04 Running on server: post build plugin 'Maven Dependencies Postprocessor'
07-Nov-2024 13:17:04 All post build plugins have finished
07-Nov-2024 13:17:04 Generating build results summary...
07-Nov-2024 13:17:04 Saving build results to disk...
07-Nov-2024 13:17:04 Logging substituted variables...
07-Nov-2024 13:17:04 Indexing build results...
07-Nov-2024 13:17:04 Finished building JB-GDL38-JOB1-2.