Started by upstream project "BIOFORMATS-test-repo" build number 249 originally caused by: Started by upstream project "Trigger" build number 273 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins4763525467099950752.sh + '[' imspector = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_39274_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] 03:52:07,905 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:52:07,906 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 03:52:07,906 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:52:07,907 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:52:07,907 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:52:07,908 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:52:07,908 |-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] 03:52:07,908 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:52:07,908 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:52:07,909 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:52:07,909 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:52:07,909 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:52:08,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:52:08,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:52:08,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:52:08,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:52:08,178 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:52:08,178 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:52:08,178 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:52:08,178 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:52:08,178 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 03:52:08,179 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 03:52:08,179 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 271 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-08 03:52:08,188] [main] java.version = 1.8.0_342 [testng] 03:52:08,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:52:08,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:52:08,234 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-08_03-52-08.log] [testng] 03:52:08,236 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-08 03:52:08,238] [main] testng.directory = /data [testng] [2024-11-08 03:52:08,238] [main] testng.configDirectory = /config [testng] [2024-11-08 03:52:08,250] [main] testng.multiplier = 1.0 [testng] [2024-11-08 03:52:08,250] [main] testng.in-memory = false [testng] [2024-11-08 03:52:08,250] [main] testng.allow-missing = false [testng] [2024-11-08 03:52:08,250] [main] user.language = en [testng] [2024-11-08 03:52:08,250] [main] user.country = ${user.country} [testng] [2024-11-08 03:52:08,250] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-08 03:52:21,585] [main] ---------------------------------------- [testng] [2024-11-08 03:52:21,585] [main] Total files: 29 [testng] [2024-11-08 03:52:21,585] [main] Scan time: 13.334 s (459 ms/file) [testng] [2024-11-08 03:52:21,585] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 28 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-08 03:52:42,780] [pool-1-thread-1] Initializing /data/qa-7936/02 - not working.msr: [testng] 03:52:42,781 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:52:42,781 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:52:42,782 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-08_03-52-42.log] [testng] 03:52:42,782 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5057e682 - End of configuration. [testng] [2024-11-08 03:52:43,260] [pool-1-thread-12] Initializing /data/qa-17102/2 channels FLIM time series.msr: [testng] 03:52:43,261 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:52:43,261 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:52:43,261 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-08_03-52-43.log] [testng] 03:52:43,262 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2664a63 - End of configuration. [testng] [2024-11-08 03:52:43,744] [pool-1-thread-11] Initializing /data/qa-7992/ArrayIndexOutOfBoundsException.msr: [testng] 03:52:43,744 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:52:43,744 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:52:43,745 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-08_03-52-43.log] [testng] 03:52:43,745 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d6a167e - End of configuration. [testng] [2024-11-08 03:52:44,240] [pool-1-thread-10] Initializing /data/qa-7936/z-TC - for LOCI.msr: [testng] 03:52:44,240 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:52:44,240 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:52:44,240 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-08_03-52-44.log] [testng] 03:52:44,241 |-INFO in ch.qos.logback.core.sift.SiftProcessor@578dd917 - End of configuration. [testng] [2024-11-08 03:52:44,715] [pool-1-thread-9] Initializing /data/qa-7992/IllegalArgumentException.msr: [testng] 03:52:44,715 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:52:44,716 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:52:44,716 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-08_03-52-44.log] [testng] 03:52:44,717 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77ae27a4 - End of configuration. [testng] [2024-11-08 03:52:45,269] [pool-1-thread-8] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel Zstack.msr: [testng] 03:52:45,269 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:52:45,269 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:52:45,270 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-08_03-52-45.log] [testng] 03:52:45,270 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f8f0670 - End of configuration. [testng] [2024-11-08 03:52:45,801] [pool-1-thread-7] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_z-stack_FLIM_TDC_C0.ome.tif: [testng] 03:52:45,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:52:45,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:52:45,803 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-08_03-52-45.log] [testng] 03:52:45,803 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10c7ce94 - End of configuration. [testng] [2024-11-08 03:52:46,712] [pool-1-thread-6] Initializing /data/qa-17102/2 channels FLIM z stack.msr: [testng] 03:52:46,713 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:52:46,713 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:52:46,713 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-08_03-52-46.log] [testng] 03:52:46,714 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1fce5be2 - End of configuration. [testng] [2024-11-08 03:52:47,204] [pool-1-thread-5] Initializing /data/qa-9468/HPDR10467U-40-VD0191-red-100pc-without-tube.msr: [testng] 03:52:47,205 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:52:47,205 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:52:47,205 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-08_03-52-47.log] [testng] 03:52:47,206 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f182e08 - End of configuration. [testng] [2024-11-08 03:52:47,679] [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] 03:52:47,679 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:52:47,679 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:52:47,680 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-08_03-52-47.log] [testng] 03:52:47,680 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55d59b97 - End of configuration. [testng] [2024-11-08 03:52:49,925] [pool-1-thread-3] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel single slice.msr: [testng] 03:52:49,925 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:52:49,925 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:52:49,925 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-08_03-52-49.log] [testng] 03:52:49,926 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6dca6ee4 - End of configuration. [testng] [2024-11-08 03:52:50,410] [pool-1-thread-2] Initializing /data/qa-4929/OMERO data/01 - urea_irf_image_TCSPC-data.msr: [testng] 03:52:50,411 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:52:50,411 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:52:50,411 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-08_03-52-50.log] [testng] 03:52:50,411 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1cd2b43f - End of configuration. [testng] [2024-11-08 03:52:56,968] [pool-1-thread-3] Initializing /data/qa-7658/Document1_13-09-25.msr: [testng] [2024-11-08 03:52:57,483] [pool-1-thread-12] Initializing /data/qa-4929/OMERO data/01 - 27hpf_f2-GFP-wt1b+rfp-flk1 - 3channel-z-stack.msr: [testng] [2024-11-08 03:52:57,986] [pool-1-thread-6] Initializing /data/paul/msr files - Paul Thomas UEA/Lifetime file.msr: [testng] [2024-11-08 03:52:58,457] [pool-1-thread-2] Initializing /data/qa-7936/01 - working.msr: [testng] [2024-11-08 03:52:58,948] [pool-1-thread-9] Initializing /data/qa-27309/181109_e3_cut.msr: [testng] [2024-11-08 03:52:59,439] [pool-1-thread-11] Initializing /data/qa-11369/01 - 770nm FITC - HybridPMT.msr: [testng] [2024-11-08 03:52:59,908] [pool-1-thread-1] Initializing /data/qa-17102/1 channel binning 8 time series.msr: [testng] [2024-11-08 03:53:00,430] [pool-1-thread-10] Initializing /data/qa-17102/1 channel binning 4 time series.msr: [testng] [2024-11-08 03:53:00,907] [pool-1-thread-5] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps.msr: [testng] [2024-11-08 03:53:01,344] [pool-1-thread-8] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel Zstack.msr: [testng] [2024-11-08 03:53:02,724] [pool-1-thread-7] Initializing /data/qa-7992/NegativeArraySizeException_small.msr: [testng] [2024-11-08 03:53:06,617] [pool-1-thread-9] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning_12-08-53_TCSPC_C0.ome.tif: [testng] [2024-11-08 03:53:07,619] [pool-1-thread-12] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning.msr: [testng] [2024-11-08 03:53:08,190] [pool-1-thread-6] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel single slice 4 tiles.msr: [testng] [2024-11-08 03:53:08,690] [pool-1-thread-1] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_FLIM_z-stack_1.msr: [testng] [2024-11-08 03:53:09,201] [pool-1-thread-10] 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: 1 minute 12 seconds Finished: SUCCESS