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Started by upstream project "BIOFORMATS-test-repo" build number 365 originally caused by: Started by upstream project "Trigger" build number 391 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@10 [BIOFORMATS-test-folder@10] $ /bin/bash -xe /tmp/jenkins10744144540612948145.sh + '[' imspector = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_58250_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 [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] 1 warning test-automated: [testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 04:00:50,282 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 04:00:50,283 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service. [testng] 04:00:50,283 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:00:50,284 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:00:50,285 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 04:00:50,285 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 04:00:50,285 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 04:00:50,285 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:00:50,286 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:00:50,286 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 04:00:50,286 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 04:00:50,287 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 04:00:50,436 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 04:00:50,436 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 04:00:50,458 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 04:00:50,458 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 04:00:50,463 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 04:00:50,463 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 04:00:50,463 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 04:00:50,463 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 04:00:50,463 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration. [testng] 04:00:50,464 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point [testng] 04:00:50,464 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 178 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-05 04:00:50,472] [main] java.version = 17.0.2 [testng] 04:00:50,475 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:00:50,475 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:00:50,513 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-05_04-00-50.log] [testng] 04:00:50,514 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration. [testng] [2025-03-05 04:00:50,516] [main] testng.directory = /data [testng] [2025-03-05 04:00:50,516] [main] testng.configDirectory = /config [testng] [2025-03-05 04:00:50,524] [main] testng.multiplier = 1.0 [testng] [2025-03-05 04:00:50,525] [main] testng.in-memory = false [testng] [2025-03-05 04:00:50,525] [main] testng.allow-missing = false [testng] [2025-03-05 04:00:50,525] [main] user.language = en [testng] [2025-03-05 04:00:50,525] [main] user.country = ${user.country} [testng] [2025-03-05 04:00:50,525] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-05 04:01:25,249] [main] ---------------------------------------- [testng] [2025-03-05 04:01:25,249] [main] Total files: 31 [testng] [2025-03-05 04:01:25,249] [main] Scan time: 34.724 s (1120 ms/file) [testng] [2025-03-05 04:01:25,249] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 29 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-05 04:02:13,312] [pool-1-thread-1] Initializing /data/paul/msr files - Paul Thomas UEA/Lifetime file.msr: [testng] 04:02:13,313 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 04:02:13,313 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:02:13,314 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-05_04-02-13.log] [testng] 04:02:13,314 |-INFO in ch.qos.logback.core.sift.SiftProcessor@240dd88a - End of configuration. [testng] [2025-03-05 04:02:14,499] [pool-1-thread-12] Initializing /data/qa-7992/NegativeArraySizeException_small.msr: [testng] 04:02:14,500 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 04:02:14,500 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:02:14,501 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-05_04-02-14.log] [testng] 04:02:14,501 |-INFO in ch.qos.logback.core.sift.SiftProcessor@95e596e - End of configuration. [testng] [2025-03-05 04:02:15,659] [pool-1-thread-11] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel Zstack.msr: [testng] 04:02:15,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 04:02:15,660 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:02:15,660 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-05_04-02-15.log] [testng] 04:02:15,661 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11b3be50 - End of configuration. [testng] [2025-03-05 04:02:16,875] [pool-1-thread-10] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel single slice 4 tiles.msr: [testng] 04:02:16,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 04:02:16,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:02:16,876 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-05_04-02-16.log] [testng] 04:02:16,876 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6880f2ab - End of configuration. [testng] [2025-03-05 04:02:18,114] [pool-1-thread-9] Initializing /data/qa-7658/Document1_13-09-25.msr: [testng] 04:02:18,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 04:02:18,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:02:18,115 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-05_04-02-18.log] [testng] 04:02:18,115 |-INFO in ch.qos.logback.core.sift.SiftProcessor@745aea39 - End of configuration. [testng] [2025-03-05 04:02:19,267] [pool-1-thread-8] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_FLIM_z-stack_1.msr: [testng] 04:02:19,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 04:02:19,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:02:19,268 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-05_04-02-19.log] [testng] 04:02:19,268 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3af22604 - End of configuration. [testng] [2025-03-05 04:02:20,563] [pool-1-thread-7] Initializing /data/qa-17102/2 channels FLIM time series.msr: [testng] 04:02:20,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 04:02:20,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:02:20,564 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-05_04-02-20.log] [testng] 04:02:20,564 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c2186be - End of configuration. [testng] [2025-03-05 04:02:21,739] [pool-1-thread-6] Initializing /data/qa-7936/01 - working.msr: [testng] 04:02:21,739 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:02:21,739 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:02:21,740 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-05_04-02-21.log] [testng] 04:02:21,740 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d241db8 - End of configuration. [testng] [2025-03-05 04:02:22,894] [pool-1-thread-5] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps.msr: [testng] 04:02:22,895 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 04:02:22,895 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:02:22,895 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-05_04-02-22.log] [testng] 04:02:22,896 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4770c504 - End of configuration. [testng] [2025-03-05 04:02:24,009] [pool-1-thread-4] Initializing /data/qa-4929/OMERO data/01 - 27hpf_f2-GFP-wt1b+rfp-flk1 - 3channel-z-stack.msr: [testng] 04:02:24,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 04:02:24,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:02:24,010 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-05_04-02-24.log] [testng] 04:02:24,010 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22c85820 - End of configuration. [testng] [2025-03-05 04:02:25,297] [pool-1-thread-3] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning.msr: [testng] 04:02:25,297 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 04:02:25,297 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:02:25,298 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-05_04-02-25.log] [testng] 04:02:25,298 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e802013 - End of configuration. [testng] [2025-03-05 04:02:26,532] [pool-1-thread-2] Initializing /data/public/zenodo-10476252/test.msr: [testng] 04:02:26,532 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:02:26,532 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:02:26,533 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-05_04-02-26.log] [testng] 04:02:26,533 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7432d7f5 - End of configuration. [testng] [2025-03-05 04:02:37,735] [pool-1-thread-1] Initializing /data/qa-9468/HPDR10467U-40-VD0191-red-100pc-without-tube.msr: [testng] [2025-03-05 04:02:38,935] [pool-1-thread-11] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel single slice.msr: [testng] [2025-03-05 04:02:40,224] [pool-1-thread-8] Initializing /data/qa-7936/z-TC - for LOCI.msr: [testng] [2025-03-05 04:02:41,450] [pool-1-thread-7] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning_12-08-53_TCSPC_C0.ome.tif: [testng] [2025-03-05 04:02:43,582] [pool-1-thread-12] Initializing /data/qa-17102/1 channel binning 8 time series.msr: [testng] [2025-03-05 04:02:44,834] [pool-1-thread-6] Initializing /data/qa-7936/02 - not working.msr: [testng] [2025-03-05 04:02:46,073] [pool-1-thread-4] Initializing /data/qa-11369/02 - 70 - 1 - tp1 - x16 TCSPC.msr: [testng] [2025-03-05 04:02:47,383] [pool-1-thread-9] Initializing /data/qa-27309/181109_e3_cut.msr: [testng] [2025-03-05 04:02:48,654] [pool-1-thread-2] Initializing /data/qa-7992/ArrayIndexOutOfBoundsException.msr: [testng] [2025-03-05 04:02:49,869] [pool-1-thread-5] Initializing /data/qa-17102/2 channels FLIM z stack.msr: [testng] [2025-03-05 04:02:50,960] [pool-1-thread-3] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel Zstack.msr: [testng] [2025-03-05 04:02:52,033] [pool-1-thread-10] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_z-stack_FLIM_TDC_C0.ome.tif: [testng] [2025-03-05 04:03:02,310] [pool-1-thread-11] 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] [2025-03-05 04:03:07,871] [pool-1-thread-9] Initializing /data/qa-11369/01 - 770nm FITC - HybridPMT.msr: [testng] [2025-03-05 04:03:09,106] [pool-1-thread-4] Initializing /data/qa-4929/OMERO data/01 - urea_irf_image_TCSPC-data.msr: [testng] [2025-03-05 04:03:10,353] [pool-1-thread-5] Initializing /data/qa-17102/1 channel binning 4 time series.msr: [testng] [2025-03-05 04:03:11,746] [pool-1-thread-3] Initializing /data/qa-7992/IllegalArgumentException.msr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1537, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 3 minutes 4 seconds Finished: SUCCESS