Started by upstream project "BIOFORMATS-test-repo" build number 282 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins10563195230666856763.sh + '[' imspector = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_44559_merge_ci -v /uod/idr/repos/curated/imspector:/data -v /uod/idr-scratch/merge-ci/curated/imspector:/config snoopycrimecop/bioformats:merge_ci -Dtestng.memory=15g -Dtestng.threadCount=12 Buildfile: /bio-formats-build/bioformats/components/test-suite/build.xml [echo] isSnapshot = true init-title: [echo] ----------=========== bio-formats-testing-framework ===========---------- init-timestamp: init: copy-resources: compile: [resolver:resolve] Resolving artifacts compile-tests: [resolver:resolve] Resolving artifacts [javac] Compiling 1 source file to /bio-formats-build/bioformats/components/test-suite/test test-automated: [testng] File leak detector installed [testng] 12:39:47,466 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 12:39:47,468 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 12:39:47,468 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:39:47,469 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:39:47,469 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 12:39:47,469 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 12:39:47,470 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 12:39:47,470 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:39:47,470 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:39:47,471 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 12:39:47,471 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 12:39:47,471 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 12:39:47,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 12:39:47,749 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 12:39:47,781 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 12:39:47,781 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 12:39:47,790 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 12:39:47,790 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 12:39:47,790 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 12:39:47,790 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 12:39:47,791 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 12:39:47,791 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 12:39:47,792 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 322 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-06 12:39:47,803] [main] java.version = 1.8.0_342 [testng] 12:39:47,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 12:39:47,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:39:47,873 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-06_12-39-47.log] [testng] 12:39:47,876 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-06 12:39:47,878] [main] testng.directory = /data [testng] [2024-12-06 12:39:47,879] [main] testng.configDirectory = /config [testng] [2024-12-06 12:39:47,893] [main] testng.multiplier = 1.0 [testng] [2024-12-06 12:39:47,893] [main] testng.in-memory = false [testng] [2024-12-06 12:39:47,893] [main] testng.allow-missing = false [testng] [2024-12-06 12:39:47,893] [main] user.language = en [testng] [2024-12-06 12:39:47,893] [main] user.country = ${user.country} [testng] [2024-12-06 12:39:47,893] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-06 12:39:58,912] [main] ---------------------------------------- [testng] [2024-12-06 12:39:58,912] [main] Total files: 29 [testng] [2024-12-06 12:39:58,912] [main] Scan time: 11.018 s (379 ms/file) [testng] [2024-12-06 12:39:58,912] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 28 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-06 12:40:15,978] [pool-1-thread-1] Initializing /data/qa-7936/02 - not working.msr: [testng] 12:40:15,978 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 12:40:15,979 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:40:15,980 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-06_12-40-15.log] [testng] 12:40:15,980 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bc9a062 - End of configuration. [testng] [2024-12-06 12:40:16,363] [pool-1-thread-12] Initializing /data/qa-17102/2 channels FLIM time series.msr: [testng] 12:40:16,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 12:40:16,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:40:16,364 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-06_12-40-16.log] [testng] 12:40:16,364 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77ae27a4 - End of configuration. [testng] [2024-12-06 12:40:16,762] [pool-1-thread-11] Initializing /data/qa-7992/ArrayIndexOutOfBoundsException.msr: [testng] 12:40:16,762 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 12:40:16,763 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:40:16,763 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-06_12-40-16.log] [testng] 12:40:16,764 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f8f0670 - End of configuration. [testng] [2024-12-06 12:40:17,072] [pool-1-thread-10] Initializing /data/qa-7936/z-TC - for LOCI.msr: [testng] 12:40:17,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 12:40:17,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:40:17,072 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-06_12-40-17.log] [testng] 12:40:17,073 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d420a7a - End of configuration. [testng] [2024-12-06 12:40:17,464] [pool-1-thread-9] Initializing /data/qa-7992/IllegalArgumentException.msr: [testng] 12:40:17,464 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 12:40:17,465 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:40:17,465 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-06_12-40-17.log] [testng] 12:40:17,465 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12d5052a - End of configuration. [testng] [2024-12-06 12:40:17,818] [pool-1-thread-8] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel Zstack.msr: [testng] 12:40:17,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 12:40:17,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:40:17,819 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-06_12-40-17.log] [testng] 12:40:17,819 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6441ed2b - End of configuration. [testng] [2024-12-06 12:40:18,122] [pool-1-thread-7] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_z-stack_FLIM_TDC_C0.ome.tif: [testng] 12:40:18,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 12:40:18,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:40:18,123 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-06_12-40-18.log] [testng] 12:40:18,123 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12ba0733 - End of configuration. [testng] [2024-12-06 12:40:18,977] [pool-1-thread-6] Initializing /data/qa-17102/2 channels FLIM z stack.msr: [testng] 12:40:18,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 12:40:18,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:40:18,977 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-06_12-40-18.log] [testng] 12:40:18,978 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f42cb43 - End of configuration. [testng] [2024-12-06 12:40:19,344] [pool-1-thread-5] Initializing /data/qa-9468/HPDR10467U-40-VD0191-red-100pc-without-tube.msr: [testng] 12:40:19,344 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 12:40:19,344 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:40:19,345 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-06_12-40-19.log] [testng] 12:40:19,345 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6466640d - End of configuration. [testng] [2024-12-06 12:40:19,755] [pool-1-thread-4] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps/02 - 500x500x105_1046x1046x57_1_875um_steps_11-34-02_PMT - PMT [PMT1] _C0.ome.tif: [testng] 12:40:19,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 12:40:19,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:40:19,756 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-06_12-40-19.log] [testng] 12:40:19,757 |-INFO in ch.qos.logback.core.sift.SiftProcessor@388977e7 - End of configuration. [testng] [2024-12-06 12:40:21,507] [pool-1-thread-3] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel single slice.msr: [testng] 12:40:21,507 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 12:40:21,507 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:40:21,508 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-06_12-40-21.log] [testng] 12:40:21,517 |-INFO in ch.qos.logback.core.sift.SiftProcessor@833e5ca - End of configuration. [testng] [2024-12-06 12:40:21,916] [pool-1-thread-2] Initializing /data/qa-4929/OMERO data/01 - urea_irf_image_TCSPC-data.msr: [testng] 12:40:21,917 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 12:40:21,917 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:40:21,917 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-06_12-40-21.log] [testng] 12:40:21,917 |-INFO in ch.qos.logback.core.sift.SiftProcessor@894295d - End of configuration. [testng] [2024-12-06 12:40:27,136] [pool-1-thread-3] Initializing /data/qa-7658/Document1_13-09-25.msr: [testng] [2024-12-06 12:40:27,579] [pool-1-thread-12] Initializing /data/paul/msr files - Paul Thomas UEA/Lifetime file.msr: [testng] [2024-12-06 12:40:27,981] [pool-1-thread-6] Initializing /data/qa-7936/01 - working.msr: [testng] [2024-12-06 12:40:28,378] [pool-1-thread-11] Initializing /data/qa-27309/181109_e3_cut.msr: [testng] [2024-12-06 12:40:28,766] [pool-1-thread-2] Initializing /data/qa-11369/01 - 770nm FITC - HybridPMT.msr: [testng] [2024-12-06 12:40:29,150] [pool-1-thread-9] Initializing /data/qa-17102/1 channel binning 8 time series.msr: [testng] [2024-12-06 12:40:29,510] [pool-1-thread-1] Initializing /data/qa-17102/1 channel binning 4 time series.msr: [testng] [2024-12-06 12:40:29,832] [pool-1-thread-10] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps.msr: [testng] [2024-12-06 12:40:30,213] [pool-1-thread-5] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel Zstack.msr: [testng] [2024-12-06 12:40:30,632] [pool-1-thread-8] Initializing /data/qa-4929/OMERO data/01 - 27hpf_f2-GFP-wt1b+rfp-flk1 - 3channel-z-stack.msr: [testng] [2024-12-06 12:40:32,042] [pool-1-thread-7] Initializing /data/qa-7992/NegativeArraySizeException_small.msr: [testng] [2024-12-06 12:40:34,546] [pool-1-thread-11] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning_12-08-53_TCSPC_C0.ome.tif: [testng] [2024-12-06 12:40:35,387] [pool-1-thread-6] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning.msr: [testng] [2024-12-06 12:40:35,872] [pool-1-thread-2] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel single slice 4 tiles.msr: [testng] [2024-12-06 12:40:36,334] [pool-1-thread-12] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_FLIM_z-stack_1.msr: [testng] [2024-12-06 12:40:36,694] [pool-1-thread-9] Initializing /data/qa-11369/02 - 70 - 1 - tp1 - x16 TCSPC.msr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1484, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 59 seconds Finished: SUCCESS