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Started by upstream project "BIOFORMATS-test-repo" build number 260 originally caused by: Started by upstream project "Trigger" build number 284 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins9562898457125006092.sh + '[' imspector = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_41078_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] 02:51:14,878 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:51:14,879 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 02:51:14,880 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:51:14,880 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:51:14,881 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:51:14,881 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:51:14,882 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:51:14,882 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:51:14,882 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:51:14,883 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:51:14,883 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:51:14,883 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:51:15,051 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:51:15,051 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:51:15,073 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:51:15,073 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:51:15,079 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:51:15,079 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:51:15,079 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:51:15,080 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:51:15,080 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 02:51:15,080 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 02:51:15,080 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 198 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-19 02:51:15,089] [main] java.version = 11.0.16 [testng] 02:51:15,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:51:15,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:51:15,135 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-19_02-51-15.log] [testng] 02:51:15,138 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-11-19 02:51:15,140] [main] testng.directory = /data [testng] [2024-11-19 02:51:15,141] [main] testng.configDirectory = /config [testng] [2024-11-19 02:51:15,154] [main] testng.multiplier = 1.0 [testng] [2024-11-19 02:51:15,156] [main] testng.in-memory = false [testng] [2024-11-19 02:51:15,156] [main] testng.allow-missing = false [testng] [2024-11-19 02:51:15,156] [main] user.language = en [testng] [2024-11-19 02:51:15,156] [main] user.country = ${user.country} [testng] [2024-11-19 02:51:15,156] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-19 02:51:27,216] [main] ---------------------------------------- [testng] [2024-11-19 02:51:27,216] [main] Total files: 29 [testng] [2024-11-19 02:51:27,216] [main] Scan time: 12.06 s (415 ms/file) [testng] [2024-11-19 02:51:27,216] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 28 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-19 02:51:46,656] [pool-1-thread-1] Initializing /data/qa-4929/OMERO data/01 - 27hpf_f2-GFP-wt1b+rfp-flk1 - 3channel-z-stack.msr: [testng] 02:51:46,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:51:46,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:51:46,659 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-19_02-51-46.log] [testng] 02:51:46,660 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ef20f95 - End of configuration. [testng] [2024-11-19 02:51:47,229] [pool-1-thread-12] Initializing /data/qa-7658/Document1_13-09-25.msr: [testng] 02:51:47,229 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:51:47,229 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:51:47,230 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-19_02-51-47.log] [testng] 02:51:47,230 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7acdac7e - End of configuration. [testng] [2024-11-19 02:51:47,640] [pool-1-thread-11] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_z-stack_FLIM_TDC_C0.ome.tif: [testng] 02:51:47,640 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:51:47,640 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:51:47,641 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-19_02-51-47.log] [testng] 02:51:47,641 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48aaf981 - End of configuration. [testng] [2024-11-19 02:51:48,542] [pool-1-thread-10] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel single slice.msr: [testng] 02:51:48,542 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:51:48,542 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:51:48,543 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-19_02-51-48.log] [testng] 02:51:48,543 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31470003 - End of configuration. [testng] [2024-11-19 02:51:49,113] [pool-1-thread-9] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel Zstack.msr: [testng] 02:51:49,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:51:49,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:51:49,114 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-19_02-51-49.log] [testng] 02:51:49,114 |-INFO in ch.qos.logback.core.sift.SiftProcessor@129fe0c7 - End of configuration. [testng] [2024-11-19 02:51:49,691] [pool-1-thread-8] 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] 02:51:49,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:51:49,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:51:49,692 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-19_02-51-49.log] [testng] 02:51:49,692 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1be192e - End of configuration. [testng] [2024-11-19 02:51:51,851] [pool-1-thread-7] Initializing /data/qa-7992/NegativeArraySizeException_small.msr: [testng] 02:51:51,851 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:51:51,851 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:51:51,851 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-19_02-51-51.log] [testng] 02:51:51,852 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e016bb5 - End of configuration. [testng] [2024-11-19 02:51:52,273] [pool-1-thread-6] Initializing /data/qa-7992/ArrayIndexOutOfBoundsException.msr: [testng] 02:51:52,274 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:51:52,274 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:51:52,274 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-19_02-51-52.log] [testng] 02:51:52,275 |-INFO in ch.qos.logback.core.sift.SiftProcessor@799b550e - End of configuration. [testng] [2024-11-19 02:51:52,699] [pool-1-thread-5] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning.msr: [testng] 02:51:52,700 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:51:52,700 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:51:52,700 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-19_02-51-52.log] [testng] 02:51:52,701 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b05fd12 - End of configuration. [testng] [2024-11-19 02:51:53,160] [pool-1-thread-4] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel single slice 4 tiles.msr: [testng] 02:51:53,160 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:51:53,160 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:51:53,160 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-19_02-51-53.log] [testng] 02:51:53,161 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64211640 - End of configuration. [testng] [2024-11-19 02:51:53,558] [pool-1-thread-3] Initializing /data/qa-27309/181109_e3_cut.msr: [testng] 02:51:53,558 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:51:53,558 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:51:53,559 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-19_02-51-53.log] [testng] 02:51:53,559 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5fdf81bb - End of configuration. [testng] [2024-11-19 02:51:53,964] [pool-1-thread-2] Initializing /data/qa-17102/2 channels FLIM time series.msr: [testng] 02:51:53,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:51:53,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:51:53,965 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-19_02-51-53.log] [testng] 02:51:53,966 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b3d1b2d - End of configuration. [testng] [2024-11-19 02:52:00,300] [pool-1-thread-3] Initializing /data/qa-7936/02 - not working.msr: [testng] [2024-11-19 02:52:00,674] [pool-1-thread-10] Initializing /data/qa-4929/OMERO data/01 - urea_irf_image_TCSPC-data.msr: [testng] [2024-11-19 02:52:01,139] [pool-1-thread-2] Initializing /data/qa-17102/1 channel binning 4 time series.msr: [testng] [2024-11-19 02:52:01,541] [pool-1-thread-7] Initializing /data/qa-7936/01 - working.msr: [testng] [2024-11-19 02:52:01,944] [pool-1-thread-1] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel Zstack.msr: [testng] [2024-11-19 02:52:02,351] [pool-1-thread-6] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning_12-08-53_TCSPC_C0.ome.tif: [testng] [2024-11-19 02:52:03,284] [pool-1-thread-12] Initializing /data/paul/msr files - Paul Thomas UEA/Lifetime file.msr: [testng] [2024-11-19 02:52:03,848] [pool-1-thread-5] Initializing /data/qa-11369/02 - 70 - 1 - tp1 - x16 TCSPC.msr: [testng] [2024-11-19 02:52:04,346] [pool-1-thread-9] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps.msr: [testng] [2024-11-19 02:52:04,912] [pool-1-thread-4] Initializing /data/qa-7992/IllegalArgumentException.msr: [testng] [2024-11-19 02:52:05,570] [pool-1-thread-11] Initializing /data/qa-9468/HPDR10467U-40-VD0191-red-100pc-without-tube.msr: [testng] [2024-11-19 02:52:09,071] [pool-1-thread-12] Initializing /data/qa-11369/01 - 770nm FITC - HybridPMT.msr: [testng] [2024-11-19 02:52:09,507] [pool-1-thread-7] Initializing /data/qa-7936/z-TC - for LOCI.msr: [testng] [2024-11-19 02:52:10,049] [pool-1-thread-2] Initializing /data/qa-17102/2 channels FLIM z stack.msr: [testng] [2024-11-19 02:52:10,471] [pool-1-thread-3] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_FLIM_z-stack_1.msr: [testng] [2024-11-19 02:52:10,946] [pool-1-thread-5] Initializing /data/qa-17102/1 channel binning 8 time series.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 6 seconds Finished: SUCCESS