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Started by upstream project "BIOFORMATS-test-repo" build number 9 originally caused by: Started by upstream project "Trigger" build number 12 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins12979325359691608627.sh + '[' imspector = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_1404_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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 01:44:48,802 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:44:48,803 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 01:44:48,803 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:44:48,805 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:44:48,805 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:44:48,805 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:44:48,806 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:44:48,806 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:44:48,806 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:44:48,807 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:44:48,807 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:44:48,807 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:44:49,016 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:44:49,016 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:44:49,040 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:44:49,040 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:44:49,045 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:44:49,045 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:44:49,046 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:44:49,046 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:44:49,046 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 01:44:49,047 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 01:44:49,047 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 241 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-23 01:44:49,057] [main] java.version = 11.0.16 [testng] 01:44:49,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:44:49,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:49,120 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-23_01-44-49.log] [testng] 01:44:49,122 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-03-23 01:44:49,124] [main] testng.directory = /data [testng] [2024-03-23 01:44:49,124] [main] testng.configDirectory = /config [testng] [2024-03-23 01:44:49,148] [main] testng.multiplier = 1.0 [testng] [2024-03-23 01:44:49,150] [main] testng.in-memory = false [testng] [2024-03-23 01:44:49,150] [main] testng.allow-missing = false [testng] [2024-03-23 01:44:49,150] [main] user.language = en [testng] [2024-03-23 01:44:49,150] [main] user.country = ${user.country} [testng] [2024-03-23 01:44:49,150] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-23 01:44:56,959] [main] ---------------------------------------- [testng] [2024-03-23 01:44:56,959] [main] Total files: 29 [testng] [2024-03-23 01:44:56,959] [main] Scan time: 7.809 s (269 ms/file) [testng] [2024-03-23 01:44:56,959] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 28 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-23 01:45:13,140] [pool-1-thread-1] Initializing /data/qa-7936/z-TC - for LOCI.msr: [testng] 01:45:13,141 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:45:13,141 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:13,144 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-23_01-45-13.log] [testng] 01:45:13,144 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57a444d3 - End of configuration. [testng] [2024-03-23 01:45:13,386] [pool-1-thread-12] Initializing /data/qa-17102/1 channel binning 8 time series.msr: [testng] 01:45:13,386 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:45:13,386 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:13,387 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-23_01-45-13.log] [testng] 01:45:13,387 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17c3db9a - End of configuration. [testng] [2024-03-23 01:45:13,884] [pool-1-thread-11] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel Zstack.msr: [testng] 01:45:13,884 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:45:13,884 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:13,885 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-23_01-45-13.log] [testng] 01:45:13,885 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bb1c538 - End of configuration. [testng] [2024-03-23 01:45:14,124] [pool-1-thread-10] Initializing /data/qa-17102/2 channels FLIM time series.msr: [testng] 01:45:14,124 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:45:14,124 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:14,125 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-23_01-45-14.log] [testng] 01:45:14,125 |-INFO in ch.qos.logback.core.sift.SiftProcessor@aba8227 - End of configuration. [testng] [2024-03-23 01:45:14,314] [pool-1-thread-9] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel single slice.msr: [testng] 01:45:14,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:45:14,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:14,314 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-23_01-45-14.log] [testng] 01:45:14,315 |-INFO in ch.qos.logback.core.sift.SiftProcessor@472e3daa - End of configuration. [testng] [2024-03-23 01:45:14,431] [pool-1-thread-8] Initializing /data/qa-7992/IllegalArgumentException.msr: [testng] 01:45:14,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:45:14,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:14,432 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-23_01-45-14.log] [testng] 01:45:14,433 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11af9f94 - End of configuration. [testng] [2024-03-23 01:45:14,756] [pool-1-thread-7] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning.msr: [testng] 01:45:14,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:45:14,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:14,757 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-23_01-45-14.log] [testng] 01:45:14,758 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28bc6d58 - End of configuration. [testng] [2024-03-23 01:45:15,011] [pool-1-thread-6] Initializing /data/qa-4929/OMERO data/01 - 27hpf_f2-GFP-wt1b+rfp-flk1 - 3channel-z-stack.msr: [testng] 01:45:15,011 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:45:15,011 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:15,013 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-23_01-45-15.log] [testng] 01:45:15,013 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ad5fde3 - End of configuration. [testng] [2024-03-23 01:45:15,265] [pool-1-thread-5] Initializing /data/qa-7992/NegativeArraySizeException_small.msr: [testng] 01:45:15,265 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:45:15,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:15,266 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-23_01-45-15.log] [testng] 01:45:15,267 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a9cc317 - End of configuration. [testng] [2024-03-23 01:45:15,440] [pool-1-thread-4] Initializing /data/qa-4929/OMERO data/01 - urea_irf_image_TCSPC-data.msr: [testng] 01:45:15,440 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:45:15,440 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:15,441 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-23_01-45-15.log] [testng] 01:45:15,441 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76f02583 - End of configuration. [testng] [2024-03-23 01:45:15,641] [pool-1-thread-3] Initializing /data/qa-7936/02 - not working.msr: [testng] 01:45:15,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:45:15,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:15,642 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-23_01-45-15.log] [testng] 01:45:15,642 |-INFO in ch.qos.logback.core.sift.SiftProcessor@80fad51 - End of configuration. [testng] [2024-03-23 01:45:15,806] [pool-1-thread-2] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_z-stack_FLIM_TDC_C0.ome.tif: [testng] 01:45:15,806 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:45:15,806 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:15,807 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-23_01-45-15.log] [testng] 01:45:15,807 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7414507a - End of configuration. [testng] [2024-03-23 01:45:19,988] [pool-1-thread-9] 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] [2024-03-23 01:45:20,688] [pool-1-thread-12] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel Zstack.msr: [testng] [2024-03-23 01:45:20,806] [pool-1-thread-5] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel single slice 4 tiles.msr: [testng] [2024-03-23 01:45:20,964] [pool-1-thread-10] Initializing /data/qa-11369/01 - 770nm FITC - HybridPMT.msr: [testng] [2024-03-23 01:45:21,089] [pool-1-thread-4] Initializing /data/paul/msr files - Paul Thomas UEA/Lifetime file.msr: [testng] [2024-03-23 01:45:21,217] [pool-1-thread-6] Initializing /data/qa-7992/ArrayIndexOutOfBoundsException.msr: [testng] [2024-03-23 01:45:21,371] [pool-1-thread-8] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps.msr: [testng] [2024-03-23 01:45:21,506] [pool-1-thread-3] Initializing /data/qa-11369/02 - 70 - 1 - tp1 - x16 TCSPC.msr: [testng] [2024-03-23 01:45:21,636] [pool-1-thread-1] Initializing /data/qa-7658/Document1_13-09-25.msr: [testng] [2024-03-23 01:45:21,815] [pool-1-thread-7] Initializing /data/qa-9468/HPDR10467U-40-VD0191-red-100pc-without-tube.msr: [testng] [2024-03-23 01:45:21,952] [pool-1-thread-11] Initializing /data/qa-27309/181109_e3_cut.msr: [testng] [2024-03-23 01:45:22,821] [pool-1-thread-2] Initializing /data/qa-17102/1 channel binning 4 time series.msr: [testng] [2024-03-23 01:45:24,157] [pool-1-thread-11] Initializing /data/qa-17102/2 channels FLIM z stack.msr: [testng] [2024-03-23 01:45:24,839] [pool-1-thread-6] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning_12-08-53_TCSPC_C0.ome.tif: [testng] [2024-03-23 01:45:25,604] [pool-1-thread-4] Initializing /data/qa-7936/01 - working.msr: [testng] [2024-03-23 01:45:25,882] [pool-1-thread-8] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_FLIM_z-stack_1.msr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1484, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 55 seconds Finished: SUCCESS