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Started by upstream project "BIOFORMATS-test-repo" build number 84 originally caused by: Started by upstream project "Trigger" build number 95 originally caused by: Started by user devspace 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/jenkins4113612225726668041.sh + '[' imspector = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_12887_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings 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] 09:49:06,750 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 09:49:06,751 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 09:49:06,751 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:49:06,752 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:49:06,753 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 09:49:06,753 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 09:49:06,753 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 09:49:06,753 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:49:06,754 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:49:06,754 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 09:49:06,754 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 09:49:06,755 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 09:49:06,909 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 09:49:06,909 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 09:49:06,934 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 09:49:06,934 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 09:49:06,940 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 09:49:06,940 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 09:49:06,940 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 09:49:06,941 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 09:49:06,941 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 09:49:06,942 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 09:49:06,942 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 188 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-06 09:49:06,950] [main] java.version = 21 [testng] 09:49:06,954 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 09:49:06,954 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:49:06,994 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-06_09-49-06.log] [testng] 09:49:06,996 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-06-06 09:49:06,997] [main] testng.directory = /data [testng] [2024-06-06 09:49:06,997] [main] testng.configDirectory = /config [testng] [2024-06-06 09:49:07,006] [main] testng.multiplier = 1.0 [testng] [2024-06-06 09:49:07,007] [main] testng.in-memory = false [testng] [2024-06-06 09:49:07,007] [main] testng.allow-missing = false [testng] [2024-06-06 09:49:07,007] [main] user.language = en [testng] [2024-06-06 09:49:07,007] [main] user.country = ${user.country} [testng] [2024-06-06 09:49:07,007] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-06 09:49:08,585] [main] ---------------------------------------- [testng] [2024-06-06 09:49:08,585] [main] Total files: 29 [testng] [2024-06-06 09:49:08,585] [main] Scan time: 1.578 s (54 ms/file) [testng] [2024-06-06 09:49:08,585] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 28 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-06 09:49:13,816] [pool-1-thread-1] 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] 09:49:13,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 09:49:13,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:49:13,817 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-06_09-49-13.log] [testng] 09:49:13,818 |-INFO in ch.qos.logback.core.sift.SiftProcessor@479b4ae - End of configuration. [testng] [2024-06-06 09:49:14,036] [pool-1-thread-12] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps.msr: [testng] 09:49:14,036 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 09:49:14,037 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:49:14,038 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-06_09-49-14.log] [testng] 09:49:14,038 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40799e61 - End of configuration. [testng] [2024-06-06 09:49:14,084] [pool-1-thread-11] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning_12-08-53_TCSPC_C0.ome.tif: [testng] 09:49:14,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 09:49:14,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:49:14,086 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-06_09-49-14.log] [testng] 09:49:14,086 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2fcf5c54 - End of configuration. [testng] [2024-06-06 09:49:14,335] [pool-1-thread-10] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel Zstack.msr: [testng] 09:49:14,335 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 09:49:14,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:49:14,336 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-06_09-49-14.log] [testng] 09:49:14,337 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23e46e2c - End of configuration. [testng] [2024-06-06 09:49:14,386] [pool-1-thread-9] Initializing /data/qa-7992/ArrayIndexOutOfBoundsException.msr: [testng] 09:49:14,386 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 09:49:14,387 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:49:14,387 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-06_09-49-14.log] [testng] 09:49:14,388 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c88220a - End of configuration. [testng] [2024-06-06 09:49:14,437] [pool-1-thread-8] Initializing /data/qa-7992/IllegalArgumentException.msr: [testng] 09:49:14,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 09:49:14,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:49:14,438 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-06_09-49-14.log] [testng] 09:49:14,438 |-INFO in ch.qos.logback.core.sift.SiftProcessor@568e058d - End of configuration. [testng] [2024-06-06 09:49:14,484] [pool-1-thread-7] Initializing /data/qa-4929/OMERO data/01 - urea_irf_image_TCSPC-data.msr: [testng] 09:49:14,484 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 09:49:14,484 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:49:14,485 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-06_09-49-14.log] [testng] 09:49:14,485 |-INFO in ch.qos.logback.core.sift.SiftProcessor@185f3b5c - End of configuration. [testng] [2024-06-06 09:49:14,526] [pool-1-thread-6] Initializing /data/qa-7992/NegativeArraySizeException_small.msr: [testng] 09:49:14,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 09:49:14,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:49:14,527 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-06_09-49-14.log] [testng] 09:49:14,527 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7da62f15 - End of configuration. [testng] [2024-06-06 09:49:14,579] [pool-1-thread-5] Initializing /data/qa-7936/01 - working.msr: [testng] 09:49:14,579 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 09:49:14,579 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:49:14,580 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-06_09-49-14.log] [testng] 09:49:14,580 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c7f1bd - End of configuration. [testng] [2024-06-06 09:49:14,623] [pool-1-thread-4] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel single slice 4 tiles.msr: [testng] 09:49:14,623 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 09:49:14,623 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:49:14,624 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-06_09-49-14.log] [testng] 09:49:14,624 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a49a326 - End of configuration. [testng] [2024-06-06 09:49:14,663] [pool-1-thread-3] Initializing /data/qa-17102/1 channel binning 4 time series.msr: [testng] 09:49:14,664 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 09:49:14,664 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:49:14,664 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-06_09-49-14.log] [testng] 09:49:14,665 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23cf4044 - End of configuration. [testng] [2024-06-06 09:49:14,687] [pool-1-thread-2] Initializing /data/qa-7936/z-TC - for LOCI.msr: [testng] 09:49:14,688 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 09:49:14,688 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:49:14,688 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-06_09-49-14.log] [testng] 09:49:14,689 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77f1f884 - End of configuration. [testng] [2024-06-06 09:49:16,922] [pool-1-thread-8] Initializing /data/qa-7936/02 - not working.msr: [testng] [2024-06-06 09:49:16,958] [pool-1-thread-6] Initializing /data/qa-17102/2 channels FLIM z stack.msr: [testng] [2024-06-06 09:49:17,002] [pool-1-thread-3] Initializing /data/qa-4929/OMERO data/01 - 27hpf_f2-GFP-wt1b+rfp-flk1 - 3channel-z-stack.msr: [testng] [2024-06-06 09:49:17,041] [pool-1-thread-9] Initializing /data/qa-9468/HPDR10467U-40-VD0191-red-100pc-without-tube.msr: [testng] [2024-06-06 09:49:17,081] [pool-1-thread-7] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_FLIM_z-stack_1.msr: [testng] [2024-06-06 09:49:17,119] [pool-1-thread-5] Initializing /data/qa-11369/02 - 70 - 1 - tp1 - x16 TCSPC.msr: [testng] [2024-06-06 09:49:17,157] [pool-1-thread-2] Initializing /data/qa-7658/Document1_13-09-25.msr: [testng] [2024-06-06 09:49:17,187] [pool-1-thread-12] Initializing /data/paul/msr files - Paul Thomas UEA/Lifetime file.msr: [testng] [2024-06-06 09:49:17,213] [pool-1-thread-10] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_z-stack_FLIM_TDC_C0.ome.tif: [testng] [2024-06-06 09:49:17,859] [pool-1-thread-12] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning.msr: [testng] [2024-06-06 09:49:17,935] [pool-1-thread-11] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel Zstack.msr: [testng] [2024-06-06 09:49:18,025] [pool-1-thread-6] Initializing /data/qa-17102/1 channel binning 8 time series.msr: [testng] [2024-06-06 09:49:18,087] [pool-1-thread-7] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel single slice.msr: [testng] [2024-06-06 09:49:18,171] [pool-1-thread-5] Initializing /data/qa-27309/181109_e3_cut.msr: [testng] [2024-06-06 09:49:18,196] [pool-1-thread-8] Initializing /data/qa-11369/01 - 770nm FITC - HybridPMT.msr: [testng] [2024-06-06 09:49:18,221] [pool-1-thread-2] Initializing /data/qa-17102/2 channels FLIM 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: 16 seconds Finished: SUCCESS