Updates the Jalview Develop 2-12 builds at https://www.jalview.org/development/jalview_develop-2-12/
Build: #7 failed
Job: Default Job failed
Build log
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| 04-Dec-2025 14:59:05 | J2S transpiling (763/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/structure/StructureCommandI.java |
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| 04-Dec-2025 14:59:07 | >>>main found for jalview.util.ProbabilityAnalyserKickstarter |
| 04-Dec-2025 14:59:07 | J2S creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/./build/jalviewjs/tmp/site_js/jalview_util_ProbabilityAnalyserKickstarter.html |
| 04-Dec-2025 14:59:07 | J2S transpiling (819/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/util/QuickSort.java |
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| 04-Dec-2025 14:59:07 | J2S transpiling (867/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/AWSThread.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (868/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/AWsJob.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (869/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/DBRefFetcher.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (870/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/HttpClientUtils.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (871/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/JobStateSummary.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (872/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/SequenceFetcher.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (873/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/ServiceChangeListener.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (874/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/WSClient.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (875/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/WSClientI.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (876/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/WSDiscovererI.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (877/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/WSMenuEntryProviderI.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (878/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/api/CancellableI.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (879/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/api/DistanceMatrixResultI.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (880/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/api/JalviewServiceEndpointProviderI.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (881/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/api/JalviewWebServiceI.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (882/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/api/JobId.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (883/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/api/MsaI.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (884/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/api/MsaResultI.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (885/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/api/MsaWithGuideTreeI.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (886/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/api/MultipleSequenceAlignmentI.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (887/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/api/SequenceAnnotationServiceI.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (888/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/api/ServiceWithParameters.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (889/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/api/TreeResultI.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (890/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/api/UIinfo.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (891/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/api/WSAnnotationCalcManagerI.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (892/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/datamodel/MappableContactMatrixI.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (893/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (894/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java |
| 04-Dec-2025 14:59:07 | J2S transpiling (895/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/EBIAlfaFold.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (896/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (897/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/EmblCdsSource.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (898/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/EmblFlatfileSource.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (899/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/EmblSource.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (900/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/EmblXmlSource.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (901/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/GeneDbSource.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (902/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/Pdb.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (903/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/Pfam.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (904/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/PfamFull.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (905/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/PfamSeed.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (906/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/Rfam.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (907/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/RfamFull.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (908/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/RfamSeed.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (909/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/TDBeacons.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (910/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/Uniprot.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (911/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/UniprotName.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (912/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/dbsources/Xfam.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (913/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/ebi/EBIFetchClient.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (914/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/ebi/HmmerJSONProcessor.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (915/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/ebi/hmmerClient.java |
| 04-Dec-2025 14:59:08 | >>>main found for jalview.ws.ebi.hmmerClient |
| 04-Dec-2025 14:59:08 | J2S creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/./build/jalviewjs/tmp/site_js/jalview_ws_ebi_hmmerClient.html |
| 04-Dec-2025 14:59:08 | J2S transpiling (916/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/gui/AnnotationWsJob.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (917/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/gui/MsaWSJob.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (918/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/gui/MsaWSThread.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (919/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/gui/WsJob.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (920/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/io/mime/HttpContentHandler.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (921/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/io/mime/JalviewMimeContentHandler.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (922/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/io/mime/MimeTypes.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (923/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws1/Annotate3D.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (924/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws1/Discoverer.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (925/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws1/JPredClient.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (926/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws1/JPredThread.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (927/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws1/JWS1Thread.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (928/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws1/MsaWSClient.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (929/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws1/MsaWSThread.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (930/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws1/SeqSearchWSClient.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (931/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws1/SeqSearchWSThread.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (932/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws1/WS1Client.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (933/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws1/WSJob.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (934/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/AWS2Thread.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (935/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/JWs2Job.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (936/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/JabaParamStore.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (937/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/JabaPreset.java |
| 04-Dec-2025 14:59:08 | J2S transpiling (938/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/JabaWsParamTest.java |
| 04-Dec-2025 14:59:08 | >>>main found for jalview.ws.jws2.JabaWsParamTest |
| 04-Dec-2025 14:59:08 | J2S creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/./build/jalviewjs/tmp/site_js/jalview_ws_jws2_JabaWsParamTest.html |
| 04-Dec-2025 14:59:08 | J2S transpiling (939/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/JabaWsServerQuery.java |
| 04-Dec-2025 14:59:10 | J2S transpiling (940/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/Jws2Client.java |
| 04-Dec-2025 14:59:10 | J2S transpiling (941/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/Jws2ClientFactory.java |
| 04-Dec-2025 14:59:10 | J2S transpiling (942/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/Jws2Discoverer.java |
| 04-Dec-2025 14:59:10 | J2S transpiling (943/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/MsaWSClient.java |
| 04-Dec-2025 14:59:10 | J2S transpiling (944/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/ParameterUtils.java |
| 04-Dec-2025 14:59:10 | J2S transpiling (945/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/PreferredServiceChangeListener.java |
| 04-Dec-2025 14:59:10 | J2S transpiling (946/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/PreferredServiceRegistry.java |
| 04-Dec-2025 14:59:10 | J2S transpiling (947/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/SeqAnnotationServiceCalcWorker.java |
| 04-Dec-2025 14:59:10 | J2S transpiling (948/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/SequenceAnnotationWSClient.java |
| 04-Dec-2025 14:59:10 | J2S transpiling (949/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/dm/AAConSettings.java |
| 04-Dec-2025 14:59:10 | J2S transpiling (950/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/dm/JabaOption.java |
| 04-Dec-2025 14:59:10 | J2S transpiling (951/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/dm/JabaParameter.java |
| 04-Dec-2025 14:59:10 | J2S transpiling (952/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/dm/JabaValueConstrain.java |
| 04-Dec-2025 14:59:10 | J2S transpiling (953/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/dm/JabaWsParamSet.java |
| 04-Dec-2025 14:59:10 | J2S transpiling (954/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/jabaws2/AAConClient.java |
| 04-Dec-2025 14:59:10 | J2S transpiling (955/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/jabaws2/AADisorderClient.java |
| 04-Dec-2025 14:59:10 | J2S transpiling (956/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/jabaws2/JabawsAnnotationInstance.java |
| 04-Dec-2025 14:59:10 | J2S transpiling (957/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/jabaws2/JabawsMsaInstance.java |
| 04-Dec-2025 14:59:10 | J2S transpiling (958/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/jabaws2/JabawsMsaInterfaceAlignCalcWorker.java |
| 04-Dec-2025 14:59:10 | J2S transpiling (959/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/jabaws2/JabawsServiceInstance.java |
| 04-Dec-2025 14:59:10 | J2S transpiling (960/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/jabaws2/Jws2Instance.java |
| 04-Dec-2025 14:59:10 | J2S transpiling (961/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java |
| 04-Dec-2025 14:59:10 | J2S transpiling (962/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/jws2/jabaws2/RNAalifoldClient.java |
| 04-Dec-2025 14:59:10 | J2S transpiling (963/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/params/ArgumentI.java |
| 04-Dec-2025 14:59:10 | J2S transpiling (964/1253) /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/src/jalview/ws/params/AutoCalcSetting.java |
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| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/urls/UrlLinkTableModelTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/urls/UrlProviderTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/ArrayUtilsTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/CaseInsensitiveStringTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/ColorUtilsTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/ComparisonTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/DBRefUtilsTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/DnaUtilsTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/FileUtilsTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/FormatTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/HMMProbabilityDistributionAnalyserTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/HttpUtilsTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/ImageMakerTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/JSONUtilsTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/LaunchUtilsTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/Log4jTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/MapListTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/MappingUtilsTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/MathUtilsTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/MessageManagerTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/ParseHtmlBodyAndLinksTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/PlatformTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/QuickSortTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/SetUtilsTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/ShiftListTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/SparseCountTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/StringUtilsTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/UrlLinkTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/dialogrunner/DialogRunnerTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/imagemaker/BitmapImageSizeTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/matcher/ConditionTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/util/matcher/MatcherTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/viewmodel/OverviewDimensionsHideHiddenTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/viewmodel/OverviewDimensionsShowHiddenTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/viewmodel/ViewportRangesTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/viewmodel/styles/ViewStyleTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/workers/AlignCaclManager2Test.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/workers/AlignCalcManagerTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws/PDBSequenceFetcherTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws/SequenceFetcherTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws/dbsources/EBIAlphaFoldTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws/dbsources/EmblXmlSourceTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws/dbsources/PfamFullTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws/dbsources/PfamSeedTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws/dbsources/RemoteFormatTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws/dbsources/RfamFullTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws/dbsources/RfamSeedTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws/dbsources/UniprotTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws/dbsources/XfamFetcherTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws/ebi/EBIFetchClientTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws/ebi/HmmerJSONProcessTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws/gui/Jws2ParamView.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws/jabaws/AAConAnnotAndSettingsIO.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws/jabaws/DisorderAnnotExportImport.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws/jabaws/MinJabawsClientTests.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws/jabaws/RNAStructExportImport.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws/jws2/ParameterUtilsTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws/rest/RestClientTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws/rest/ShmmrRSBSService.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws/seqfetcher/DbRefFetcherTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws/sifts/SiftsClientTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws/utils/UrlDownloadClientTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws2/actions/alignment/AlignmentActionTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws2/actions/annotation/AnnotationJobTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws2/actions/secstructpred/SecStructPredMsaTaskTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws2/actions/secstructpred/SecStructPredPDBSearchTaskTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/jalview/ws2/client/slivka/SlivkaWSDiscovererTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/junit/extensions/PA.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/junit/extensions/PrivilegedAccessor.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/mc_view/AtomTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/mc_view/BondTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/mc_view/PDBChainTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/mc_view/PDBfileTest.java |
| 04-Dec-2025 14:59:13 | J2S excluded /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/test/mc_view/ResidueTest.java |
| 04-Dec-2025 14:59:13 | J2S processed 1253 .java files, created 1285 .js files and 11 .html files, copied 7 resources |
| 04-Dec-2025 14:59:13 | J2S buildFinished 1253 files transpiled for /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1 |
| 04-Dec-2025 14:59:13 | J2S buildFinished nerror = 0 Thu Dec 04 14:59:13 GMT 2025 |
| 04-Dec-2025 14:59:13 | (Found 4 errors + 3202 warnings) Build done |
| 04-Dec-2025 14:59:13 | Invoking 'Gradle Project Builder' on '/jalview'. |
| 04-Dec-2025 14:59:15 | :jalviewjsTranspile (Thread[Execution worker for ':',5,main]) completed. Took 1 mins 27.408 secs. |
| 04-Dec-2025 14:59:15 | :jalviewjsCopyTransferSiteJs (Thread[Execution worker for ':',5,main]) started. |
| 04-Dec-2025 14:59:15 | |
| 04-Dec-2025 14:59:15 | > Task :jalviewjsCopyTransferSiteJs |
| 04-Dec-2025 14:59:15 | Caching disabled for task ':jalviewjsCopyTransferSiteJs' because: |
| 04-Dec-2025 14:59:15 | Build cache is disabled |
| 04-Dec-2025 14:59:15 | Task ':jalviewjsCopyTransferSiteJs' is not up-to-date because: |
| 04-Dec-2025 14:59:15 | Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/site has been removed. |
| 04-Dec-2025 14:59:15 | Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/site/com_stevesoft_pat_RegexWriter.html has been removed. |
| 04-Dec-2025 14:59:15 | Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/site/jalview_bin_AppletParams.html has been removed. |
| 04-Dec-2025 14:59:15 | :jalviewjsCopyTransferSiteJs (Thread[Execution worker for ':',5,main]) completed. Took 0.402 secs. |
| 04-Dec-2025 14:59:15 | :jalviewjsTransferUnzipLib (Thread[Execution worker for ':',5,main]) started. |
| 04-Dec-2025 14:59:15 | |
| 04-Dec-2025 14:59:15 | > Task :jalviewjsTransferUnzipLib |
| 04-Dec-2025 14:59:15 | Caching disabled for task ':jalviewjsTransferUnzipLib' because: |
| 04-Dec-2025 14:59:15 | Build cache is disabled |
| 04-Dec-2025 14:59:15 | Task ':jalviewjsTransferUnzipLib' is not up-to-date because: |
| 04-Dec-2025 14:59:15 | Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/tmp/site_lib has been removed. |
| 04-Dec-2025 14:59:15 | Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/tmp/site_lib/fr_orsay_lri_varna_applications_AlignmentDemo.html has been removed. |
| 04-Dec-2025 14:59:15 | Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/tmp/site_lib/fr_orsay_lri_varna_applications_fragseq_FragSeqGUI.html has been removed. |
| 04-Dec-2025 14:59:15 | :jalviewjsTransferUnzipLib (Thread[Execution worker for ':',5,main]) completed. Took 0.562 secs. |
| 04-Dec-2025 14:59:15 | :jalviewjsTransferUnzipSwingJs (Thread[Execution worker for ':',5,main]) started. |
| 04-Dec-2025 14:59:16 | |
| 04-Dec-2025 14:59:16 | > Task :jalviewjsTransferUnzipSwingJs |
| 04-Dec-2025 14:59:16 | Caching disabled for task ':jalviewjsTransferUnzipSwingJs' because: |
| 04-Dec-2025 14:59:16 | Build cache is disabled |
| 04-Dec-2025 14:59:16 | Task ':jalviewjsTransferUnzipSwingJs' is not up-to-date because: |
| 04-Dec-2025 14:59:16 | Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/tmp/site_swingjs has been removed. |
| 04-Dec-2025 14:59:16 | Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/tmp/site_swingjs/___j2sflags.htm has been removed. |
| 04-Dec-2025 14:59:16 | Output property '$1' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/tmp/site_swingjs/debug.log has been removed. |
| 04-Dec-2025 14:59:16 | :jalviewjsTransferUnzipSwingJs (Thread[Execution worker for ':',5,main]) completed. Took 0.81 secs. |
| 04-Dec-2025 14:59:16 | :jalviewjsTransferUnzipAllLibs (Thread[Execution worker for ':',5,main]) started. |
| 04-Dec-2025 14:59:16 | |
| 04-Dec-2025 14:59:16 | > Task :jalviewjsTransferUnzipAllLibs |
| 04-Dec-2025 14:59:16 | Skipping task ':jalviewjsTransferUnzipAllLibs' as it has no actions. |
| 04-Dec-2025 14:59:16 | :jalviewjsTransferUnzipAllLibs (Thread[Execution worker for ':',5,main]) completed. Took 0.0 secs. |
| 04-Dec-2025 14:59:16 | :jalviewjsSyncAllLibs (Thread[Execution worker for ':',5,main]) started. |
| 04-Dec-2025 14:59:18 | |
| 04-Dec-2025 14:59:18 | > Task :jalviewjsSyncAllLibs |
| 04-Dec-2025 14:59:18 | Caching disabled for task ':jalviewjsSyncAllLibs' because: |
| 04-Dec-2025 14:59:18 | Build cache is disabled |
| 04-Dec-2025 14:59:18 | Task ':jalviewjsSyncAllLibs' is not up-to-date because: |
| 04-Dec-2025 14:59:18 | Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/site/swingjs/j2s/javajs/async/Assets.js has changed. |
| 04-Dec-2025 14:59:18 | Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/site/swingjs/j2s/javajs/async/Async.js has changed. |
| 04-Dec-2025 14:59:18 | Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/site/swingjs/j2s/javajs/async/AsyncColorChooser.js has changed. |
| 04-Dec-2025 14:59:18 | :jalviewjsSyncAllLibs (Thread[Execution worker for ':',5,main]) completed. Took 1.567 secs. |
| 04-Dec-2025 14:59:18 | :copyResources (Thread[Execution worker for ':',5,main]) started. |
| 04-Dec-2025 14:59:18 | |
| 04-Dec-2025 14:59:18 | > Task :copyResources UP-TO-DATE |
| 04-Dec-2025 14:59:18 | Caching disabled for task ':copyResources' because: |
| 04-Dec-2025 14:59:18 | Build cache is disabled |
| 04-Dec-2025 14:59:18 | Skipping task ':copyResources' as it is up-to-date. |
| 04-Dec-2025 14:59:18 | :copyResources (Thread[Execution worker for ':',5,main]) completed. Took 0.021 secs. |
| 04-Dec-2025 14:59:18 | :createBuildProperties (Thread[Execution worker for ':',5,main]) started. |
| 04-Dec-2025 14:59:18 | |
| 04-Dec-2025 14:59:18 | > Task :createBuildProperties |
| 04-Dec-2025 14:59:18 | Caching disabled for task ':createBuildProperties' because: |
| 04-Dec-2025 14:59:18 | Build cache is disabled |
| 04-Dec-2025 14:59:18 | Task ':createBuildProperties' is not up-to-date because: |
| 04-Dec-2025 14:59:18 | Value of input property 'comment' has changed for task ':createBuildProperties' |
| 04-Dec-2025 14:59:18 | Value of input property 'properties' has changed for task ':createBuildProperties' |
| 04-Dec-2025 14:59:18 | :createBuildProperties (Thread[Execution worker for ':',5,main]) completed. Took 0.002 secs. |
| 04-Dec-2025 14:59:18 | :jalviewjsSyncBuildProperties (Thread[Execution worker for ':',5,main]) started. |
| 04-Dec-2025 14:59:18 | |
| 04-Dec-2025 14:59:18 | > Task :jalviewjsSyncBuildProperties |
| 04-Dec-2025 14:59:18 | Caching disabled for task ':jalviewjsSyncBuildProperties' because: |
| 04-Dec-2025 14:59:18 | Build cache is disabled |
| 04-Dec-2025 14:59:18 | Task ':jalviewjsSyncBuildProperties' is not up-to-date because: |
| 04-Dec-2025 14:59:18 | Output property 'destinationDir' file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/site/swingjs/j2s/.build_properties has been removed. |
| 04-Dec-2025 14:59:18 | :jalviewjsSyncBuildProperties (Thread[Execution worker for ':',5,main]) completed. Took 0.116 secs. |
| 04-Dec-2025 14:59:18 | :jalviewjsBuildAllCores (Thread[Execution worker for ':',5,main]) started. |
| 04-Dec-2025 14:59:20 | |
| 04-Dec-2025 14:59:20 | > Task :jalviewjsBuildAllCores |
| 04-Dec-2025 14:59:20 | Execution optimizations have been disabled for task ':jalviewjsBuildAllCores' to ensure correctness due to the following reasons: |
| 04-Dec-2025 14:59:20 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build/jalviewjs/tmp/site_lib/swingjs/j2s'. Reason: Task ':jalviewjsBuildAllCores' uses this output of task ':jalviewjsTransferUnzipLib' 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. |
| 04-Dec-2025 14:59:20 | Invalidating VFS because task ':jalviewjsBuildAllCores' failed validation |
| 04-Dec-2025 14:59:20 | Caching disabled for task ':jalviewjsBuildAllCores' because: |
| 04-Dec-2025 14:59:20 | Build cache is disabled |
| 04-Dec-2025 14:59:20 | Task ':jalviewjsBuildAllCores' is not up-to-date because: |
| 04-Dec-2025 14:59:20 | Incremental execution has been disabled to ensure correctness. Please consult deprecation warnings for more details. |
| 04-Dec-2025 14:59:20 | Creating core for stevesoft... |
| 04-Dec-2025 14:59:20 | Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corestevesoft.js |
| 04-Dec-2025 14:59:20 | Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corestevesoft.z.js |
| 04-Dec-2025 14:59:20 | |
| 04-Dec-2025 14:59:20 | Running '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/tools/closure_compiler.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE_OPTIMIZATIONS --warning_level QUIET --charset UTF-8 --js ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corestevesoft.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corestevesoft.z.js' |
| 04-Dec-2025 14:59:20 | |
| 04-Dec-2025 14:59:20 | Starting process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java''. Working directory: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1 Command: /srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/tools/closure_compiler.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE_OPTIMIZATIONS --warning_level QUIET --charset UTF-8 --js ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corestevesoft.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corestevesoft.z.js |
| 04-Dec-2025 14:59:20 | Successfully started process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java'' |
| 04-Dec-2025 14:59:21 | -- |
| 04-Dec-2025 14:59:21 | Creating core for jvjmol... |
| 04-Dec-2025 14:59:21 | Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejvjmol.js |
| 04-Dec-2025 14:59:21 | Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejvjmol.z.js |
| 04-Dec-2025 14:59:21 | |
| 04-Dec-2025 14:59:21 | Running '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/tools/closure_compiler.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE_OPTIMIZATIONS --warning_level QUIET --charset UTF-8 --js ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejvjmol.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejvjmol.z.js' |
| 04-Dec-2025 14:59:21 | |
| 04-Dec-2025 14:59:21 | Starting process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java''. Working directory: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1 Command: /srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/tools/closure_compiler.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE_OPTIMIZATIONS --warning_level QUIET --charset UTF-8 --js ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejvjmol.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejvjmol.z.js |
| 04-Dec-2025 14:59:21 | Successfully started process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java'' |
| 04-Dec-2025 14:59:25 | -- |
| 04-Dec-2025 14:59:25 | Creating core for jalview... |
| 04-Dec-2025 14:59:25 | Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejalview.js |
| 04-Dec-2025 14:59:25 | Generating ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejalview.z.js |
| 04-Dec-2025 14:59:25 | |
| 04-Dec-2025 14:59:25 | Running '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/tools/closure_compiler.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE_OPTIMIZATIONS --warning_level QUIET --charset UTF-8 --js ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejalview.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejalview.z.js' |
| 04-Dec-2025 14:59:25 | |
| 04-Dec-2025 14:59:25 | Starting process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java''. Working directory: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1 Command: /srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/tools/closure_compiler.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE_OPTIMIZATIONS --warning_level QUIET --charset UTF-8 --js ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejalview.js --js_output_file ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejalview.z.js |
| 04-Dec-2025 14:59:25 | Successfully started process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java'' |
| 04-Dec-2025 14:59:26 | ./build/jalviewjs/tmp/site_core/swingjs/j2s/core/corejalview.js:10508: ERROR - Parse error. missing ) after argument list |
| 04-Dec-2025 14:59:26 | }}, 1); |
| 04-Dec-2025 14:59:26 | ^ |
| 04-Dec-2025 14:59:26 | |
| 04-Dec-2025 14:59:26 | 1 error(s), 0 warning(s) |
| 04-Dec-2025 14:59:26 | |
| 04-Dec-2025 14:59:26 | > Task :jalviewjsBuildAllCores FAILED |
| 04-Dec-2025 14:59:26 | :jalviewjsBuildAllCores (Thread[Execution worker for ':',5,main]) completed. Took 8.377 secs. |
| 04-Dec-2025 14:59:27 | |
| 04-Dec-2025 14:59:27 | |
| 04-Dec-2025 14:59:27 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 04-Dec-2025 14:59:27 | |
| 04-Dec-2025 14:59:27 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 04-Dec-2025 14:59:27 | |
| 04-Dec-2025 14:59:27 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 04-Dec-2025 14:59:27 | |
| 04-Dec-2025 14:59:27 | Execution optimizations have been disabled for 1 invalid unit(s) of work during this build to ensure correctness. |
| 04-Dec-2025 14:59:27 | Please consult deprecation warnings for more details. |
| 04-Dec-2025 14:59:27 | 18 actionable tasks: 16 executed, 2 up-to-date |
| 04-Dec-2025 14:59:27 | FAILURE: Build failed with an exception. |
| 04-Dec-2025 14:59:27 | |
| 04-Dec-2025 14:59:27 | * Where: |
| 04-Dec-2025 14:59:27 | Build file '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDC330-JOB1/build.gradle' line: 3944 |
| 04-Dec-2025 14:59:27 | |
| 04-Dec-2025 14:59:27 | * What went wrong: |
| 04-Dec-2025 14:59:27 | Execution failed for task ':jalviewjsBuildAllCores'. |
| 04-Dec-2025 14:59:27 | > Process 'command '/srv/bamboo/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/bin/java'' finished with non-zero exit value 1 |
| 04-Dec-2025 14:59:27 | |
| 04-Dec-2025 14:59:27 | * Try: |
| 04-Dec-2025 14:59:27 | > Run with --stacktrace option to get the stack trace. |
| 04-Dec-2025 14:59:27 | > Run with --debug option to get more log output. |
| 04-Dec-2025 14:59:27 | > Run with --scan to get full insights. |
| 04-Dec-2025 14:59:27 | |
| 04-Dec-2025 14:59:27 | * Get more help at https://help.gradle.org |
| 04-Dec-2025 14:59:27 | |
| 04-Dec-2025 14:59:27 | BUILD FAILED in 1m 54s |
| 04-Dec-2025 14:59:27 | |
| 04-Dec-2025 14:59:27 | Failing task since return code of [/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=DEVELOP-2-12 -PJAVA_VERSION=11 -Pjalviewjs_eclipse_root=~/buildtools/eclipse/latest -Pbamboo_planKey=JB-GDC330 --info eclipse jalviewjsCreateJ2sSettings jalviewjs] was 1 while expected 0 |
| 04-Dec-2025 14:59:27 | Finished task 'JalviewJS ${bamboo.CHANNEL} release' with result: Failed |
| 04-Dec-2025 14:59:27 | Running post build plugin 'NCover Results Collector' |
| 04-Dec-2025 14:59:27 | Running post build plugin 'Artifact Copier' |
| 04-Dec-2025 14:59:27 | Publishing an artifact: develop_channel_executable_jar |
| 04-Dec-2025 14:59:27 | Unable to publish artifact [develop_channel_executable_jar]: |
| 04-Dec-2025 14:59:27 | The artifact hasn't been successfully published after 20.03 ms |
| 04-Dec-2025 14:59:27 | Publishing an artifact: develop_jalview-js-site_tar |
| 04-Dec-2025 14:59:27 | Unable to publish artifact [develop_jalview-js-site_tar]: |
| 04-Dec-2025 14:59:27 | The artifact hasn't been successfully published after 2.534 ms |
| 04-Dec-2025 14:59:27 | Publishing an artifact: getdown_develop_channel_tar |
| 04-Dec-2025 14:59:27 | Unable to publish artifact [getdown_develop_channel_tar]: |
| 04-Dec-2025 14:59:27 | The artifact hasn't been successfully published after 3.195 ms |
| 04-Dec-2025 14:59:27 | Running post build plugin 'Artifactory Release Management Staging' |
| 04-Dec-2025 14:59:27 | Running post build plugin 'Artifactory Build Info Copier' |
| 04-Dec-2025 14:59:27 | Running post build plugin 'Artifactory Gradle Properties Info Copier' |
| 04-Dec-2025 14:59:27 | Running post build plugin 'npm Cache Cleanup' |
| 04-Dec-2025 14:59:27 | Running post build plugin 'Clover Results Collector' |
| 04-Dec-2025 14:59:27 | Running post build plugin 'Docker Container Cleanup' |
| 04-Dec-2025 14:59:27 | Finalising the build... |
| 04-Dec-2025 14:59:27 | Stopping timer. |
| 04-Dec-2025 14:59:27 | Build JB-GDC330-JOB1-7 completed. |
| 04-Dec-2025 14:59:27 | Running on server: post build plugin 'NCover Results Collector' |
| 04-Dec-2025 14:59:27 | Running on server: post build plugin 'Build Hanging Detection Configuration' |
| 04-Dec-2025 14:59:27 | Running on server: post build plugin 'Clover Delta Calculator' |
| 04-Dec-2025 14:59:27 | Running on server: post build plugin 'Maven Dependencies Postprocessor' |
| 04-Dec-2025 14:59:27 | All post build plugins have finished |
| 04-Dec-2025 14:59:27 | Generating build results summary... |
| 04-Dec-2025 14:59:27 | Saving build results to disk... |
| 04-Dec-2025 14:59:27 | Logging substituted variables... |
| 04-Dec-2025 14:59:27 | Indexing build results... |
| 04-Dec-2025 14:59:27 | Finished building JB-GDC330-JOB1-7. |