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Started by upstream project "BIOFORMATS-test-repo" build number 22 originally caused by: Started by upstream project "Trigger" build number 25 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/jenkins12528848196816113176.sh + '[' imspector = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_2718_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 02:15:53,385 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:15:53,387 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 02:15:53,387 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:15:53,388 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:15:53,388 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:15:53,389 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:15:53,389 |-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] 02:15:53,389 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:15:53,389 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:15:53,390 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:15:53,390 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:15:53,391 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:15:53,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:15:53,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:15:53,590 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:15:53,591 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:15:53,599 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:15:53,599 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:15:53,599 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:15:53,600 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:15:53,600 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 02:15:53,602 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 02:15:53,602 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 213 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-04 02:15:53,614] [main] java.version = 21 [testng] 02:15:53,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:15:53,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:53,663 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-04_02-15-53.log] [testng] 02:15:53,664 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-04-04 02:15:53,667] [main] testng.directory = /data [testng] [2024-04-04 02:15:53,667] [main] testng.configDirectory = /config [testng] [2024-04-04 02:15:53,676] [main] testng.multiplier = 1.0 [testng] [2024-04-04 02:15:53,677] [main] testng.in-memory = false [testng] [2024-04-04 02:15:53,677] [main] testng.allow-missing = false [testng] [2024-04-04 02:15:53,677] [main] user.language = en [testng] [2024-04-04 02:15:53,677] [main] user.country = ${user.country} [testng] [2024-04-04 02:15:53,677] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-04-04 02:15:55,318] [main] ---------------------------------------- [testng] [2024-04-04 02:15:55,318] [main] Total files: 29 [testng] [2024-04-04 02:15:55,318] [main] Scan time: 1.641 s (56 ms/file) [testng] [2024-04-04 02:15:55,318] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 28 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-04 02:16:00,893] [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] 02:16:00,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:16:00,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:00,894 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-04_02-16-00.log] [testng] 02:16:00,894 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29089ec7 - End of configuration. [testng] [2024-04-04 02:16:01,083] [pool-1-thread-12] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps.msr: [testng] 02:16:01,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:16:01,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:01,084 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-04_02-16-01.log] [testng] 02:16:01,084 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e1192dd - End of configuration. [testng] [2024-04-04 02:16:01,123] [pool-1-thread-11] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning_12-08-53_TCSPC_C0.ome.tif: [testng] 02:16:01,124 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:16:01,124 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:01,124 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-04_02-16-01.log] [testng] 02:16:01,125 |-INFO in ch.qos.logback.core.sift.SiftProcessor@701e253c - End of configuration. [testng] [2024-04-04 02:16:01,339] [pool-1-thread-10] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel Zstack.msr: [testng] 02:16:01,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:16:01,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:01,340 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-04_02-16-01.log] [testng] 02:16:01,340 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e020848 - End of configuration. [testng] [2024-04-04 02:16:01,369] [pool-1-thread-9] Initializing /data/qa-7992/ArrayIndexOutOfBoundsException.msr: [testng] 02:16:01,369 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:16:01,369 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:01,369 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-04_02-16-01.log] [testng] 02:16:01,370 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14a6093a - End of configuration. [testng] [2024-04-04 02:16:01,406] [pool-1-thread-8] Initializing /data/qa-7992/IllegalArgumentException.msr: [testng] 02:16:01,406 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:16:01,406 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:01,407 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-04_02-16-01.log] [testng] 02:16:01,408 |-INFO in ch.qos.logback.core.sift.SiftProcessor@185f3b5c - End of configuration. [testng] [2024-04-04 02:16:01,440] [pool-1-thread-7] Initializing /data/qa-4929/OMERO data/01 - urea_irf_image_TCSPC-data.msr: [testng] 02:16:01,441 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:16:01,441 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:01,442 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-04_02-16-01.log] [testng] 02:16:01,442 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c7f1bd - End of configuration. [testng] [2024-04-04 02:16:01,473] [pool-1-thread-6] Initializing /data/qa-7992/NegativeArraySizeException_small.msr: [testng] 02:16:01,474 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:16:01,474 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:01,474 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-04_02-16-01.log] [testng] 02:16:01,475 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a49a326 - End of configuration. [testng] [2024-04-04 02:16:01,501] [pool-1-thread-5] Initializing /data/qa-7936/01 - working.msr: [testng] 02:16:01,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:16:01,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:01,503 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-04_02-16-01.log] [testng] 02:16:01,503 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23cf4044 - End of configuration. [testng] [2024-04-04 02:16:01,535] [pool-1-thread-4] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel single slice 4 tiles.msr: [testng] 02:16:01,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:16:01,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:01,536 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-04_02-16-01.log] [testng] 02:16:01,537 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77f1f884 - End of configuration. [testng] [2024-04-04 02:16:01,577] [pool-1-thread-3] Initializing /data/qa-17102/1 channel binning 4 time series.msr: [testng] 02:16:01,577 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:16:01,577 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:01,578 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-04_02-16-01.log] [testng] 02:16:01,578 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b249504 - End of configuration. [testng] [2024-04-04 02:16:01,600] [pool-1-thread-2] Initializing /data/qa-7936/z-TC - for LOCI.msr: [testng] 02:16:01,600 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:16:01,600 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:01,601 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-04_02-16-01.log] [testng] 02:16:01,601 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2fb2eb6 - End of configuration. [testng] [2024-04-04 02:16:03,509] [pool-1-thread-3] Initializing /data/qa-7936/02 - not working.msr: [testng] [2024-04-04 02:16:03,542] [pool-1-thread-5] Initializing /data/qa-17102/2 channels FLIM z stack.msr: [testng] [2024-04-04 02:16:03,580] [pool-1-thread-7] Initializing /data/qa-4929/OMERO data/01 - 27hpf_f2-GFP-wt1b+rfp-flk1 - 3channel-z-stack.msr: [testng] [2024-04-04 02:16:03,614] [pool-1-thread-8] Initializing /data/qa-9468/HPDR10467U-40-VD0191-red-100pc-without-tube.msr: [testng] [2024-04-04 02:16:03,646] [pool-1-thread-6] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_FLIM_z-stack_1.msr: [testng] [2024-04-04 02:16:03,673] [pool-1-thread-9] Initializing /data/qa-11369/02 - 70 - 1 - tp1 - x16 TCSPC.msr: [testng] [2024-04-04 02:16:03,698] [pool-1-thread-2] Initializing /data/qa-7658/Document1_13-09-25.msr: [testng] [2024-04-04 02:16:03,737] [pool-1-thread-12] Initializing /data/paul/msr files - Paul Thomas UEA/Lifetime file.msr: [testng] [2024-04-04 02:16:03,758] [pool-1-thread-10] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_z-stack_FLIM_TDC_C0.ome.tif: [testng] [2024-04-04 02:16:04,336] [pool-1-thread-4] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning.msr: [testng] [2024-04-04 02:16:04,511] [pool-1-thread-12] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel Zstack.msr: [testng] [2024-04-04 02:16:04,562] [pool-1-thread-5] Initializing /data/qa-17102/1 channel binning 8 time series.msr: [testng] [2024-04-04 02:16:04,602] [pool-1-thread-6] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel single slice.msr: [testng] [2024-04-04 02:16:04,642] [pool-1-thread-7] Initializing /data/qa-27309/181109_e3_cut.msr: [testng] [2024-04-04 02:16:04,671] [pool-1-thread-9] Initializing /data/qa-11369/01 - 770nm FITC - HybridPMT.msr: [testng] [2024-04-04 02:16:04,696] [pool-1-thread-3] 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: 15 seconds Finished: SUCCESS