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Started by upstream project "BIOFORMATS-test-repo" build number 1 originally caused by: Started by upstream project "Trigger" build number 1 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins13859186764598224001.sh + '[' imspector = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_124_merge_ci -v /uod/idr/repos/curated/imspector:/data -v /uod/idr-scratch/devspace/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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 17:13:38,555 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 17:13:38,556 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 17:13:38,556 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 17:13:38,557 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 17:13:38,558 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 17:13:38,558 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 17:13:38,559 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 17:13:38,559 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 17:13:38,559 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 17:13:38,560 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 17:13:38,560 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 17:13:38,560 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 17:13:38,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 17:13:38,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 17:13:38,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 17:13:38,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 17:13:38,789 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 17:13:38,790 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 17:13:38,790 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 17:13:38,790 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 17:13:38,790 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 17:13:38,791 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 17:13:38,791 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 232 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-14 17:13:38,801] [main] java.version = 21 [testng] 17:13:38,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 17:13:38,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:13:38,851 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-14_17-13-38.log] [testng] 17:13:38,852 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-03-14 17:13:38,854] [main] testng.directory = /data [testng] [2024-03-14 17:13:38,855] [main] testng.configDirectory = /config [testng] [2024-03-14 17:13:38,864] [main] testng.multiplier = 1.0 [testng] [2024-03-14 17:13:38,865] [main] testng.in-memory = false [testng] [2024-03-14 17:13:38,865] [main] testng.allow-missing = false [testng] [2024-03-14 17:13:38,865] [main] user.language = en [testng] [2024-03-14 17:13:38,865] [main] user.country = ${user.country} [testng] [2024-03-14 17:13:38,865] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-14 17:13:45,991] [main] ---------------------------------------- [testng] [2024-03-14 17:13:45,991] [main] Total files: 29 [testng] [2024-03-14 17:13:45,991] [main] Scan time: 7.125 s (245 ms/file) [testng] [2024-03-14 17:13:45,992] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 28 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-14 17:13:58,587] [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] 17:13:58,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 17:13:58,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:13:58,589 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-14_17-13-58.log] [testng] 17:13:58,589 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e527d00 - End of configuration. [testng] [2024-03-14 17:14:00,159] [pool-1-thread-12] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps.msr: [testng] 17:14:00,159 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 17:14:00,159 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:14:00,161 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-14_17-14-00.log] [testng] 17:14:00,161 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2693ff2f - End of configuration. [testng] [2024-03-14 17:14:00,510] [pool-1-thread-11] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning_12-08-53_TCSPC_C0.ome.tif: [testng] 17:14:00,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 17:14:00,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:14:00,511 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-14_17-14-00.log] [testng] 17:14:00,512 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23e46e2c - End of configuration. [testng] [2024-03-14 17:14:01,161] [pool-1-thread-10] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel Zstack.msr: [testng] 17:14:01,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 17:14:01,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:14:01,162 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-14_17-14-01.log] [testng] 17:14:01,162 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d4a58b4 - End of configuration. [testng] [2024-03-14 17:14:01,371] [pool-1-thread-9] Initializing /data/qa-7992/ArrayIndexOutOfBoundsException.msr: [testng] 17:14:01,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 17:14:01,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:14:01,372 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-14_17-14-01.log] [testng] 17:14:01,372 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5421047a - End of configuration. [testng] [2024-03-14 17:14:01,626] [pool-1-thread-8] Initializing /data/qa-7992/IllegalArgumentException.msr: [testng] 17:14:01,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 17:14:01,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:14:01,628 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-14_17-14-01.log] [testng] 17:14:01,628 |-INFO in ch.qos.logback.core.sift.SiftProcessor@787f14d1 - End of configuration. [testng] [2024-03-14 17:14:01,865] [pool-1-thread-7] Initializing /data/qa-4929/OMERO data/01 - urea_irf_image_TCSPC-data.msr: [testng] 17:14:01,865 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 17:14:01,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:14:01,867 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-14_17-14-01.log] [testng] 17:14:01,867 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d2fb4ba - End of configuration. [testng] [2024-03-14 17:14:02,050] [pool-1-thread-6] Initializing /data/qa-7992/NegativeArraySizeException_small.msr: [testng] 17:14:02,051 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 17:14:02,051 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:14:02,052 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-14_17-14-02.log] [testng] 17:14:02,052 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b967cc9 - End of configuration. [testng] [2024-03-14 17:14:02,259] [pool-1-thread-5] Initializing /data/qa-7936/01 - working.msr: [testng] 17:14:02,259 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 17:14:02,259 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:14:02,260 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-14_17-14-02.log] [testng] 17:14:02,260 |-INFO in ch.qos.logback.core.sift.SiftProcessor@833018a - End of configuration. [testng] [2024-03-14 17:14:02,447] [pool-1-thread-4] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel single slice 4 tiles.msr: [testng] 17:14:02,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 17:14:02,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:14:02,448 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-14_17-14-02.log] [testng] 17:14:02,448 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c782e54 - End of configuration. [testng] [2024-03-14 17:14:02,609] [pool-1-thread-3] Initializing /data/qa-17102/1 channel binning 4 time series.msr: [testng] 17:14:02,609 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 17:14:02,609 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:14:02,610 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-14_17-14-02.log] [testng] 17:14:02,610 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f449a0e - End of configuration. [testng] [2024-03-14 17:14:02,800] [pool-1-thread-2] Initializing /data/qa-7936/z-TC - for LOCI.msr: [testng] 17:14:02,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 17:14:02,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:14:02,801 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-14_17-14-02.log] [testng] 17:14:02,801 |-INFO in ch.qos.logback.core.sift.SiftProcessor@185f3b5c - End of configuration. [testng] [2024-03-14 17:14:06,702] [pool-1-thread-3] Initializing /data/qa-7936/02 - not working.msr: [testng] [2024-03-14 17:14:06,963] [pool-1-thread-7] Initializing /data/qa-4929/OMERO data/01 - 27hpf_f2-GFP-wt1b+rfp-flk1 - 3channel-z-stack.msr: [testng] [2024-03-14 17:14:07,138] [pool-1-thread-6] Initializing /data/qa-9468/HPDR10467U-40-VD0191-red-100pc-without-tube.msr: [testng] [2024-03-14 17:14:07,395] [pool-1-thread-5] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_FLIM_z-stack_1.msr: [testng] [2024-03-14 17:14:07,594] [pool-1-thread-9] Initializing /data/qa-11369/02 - 70 - 1 - tp1 - x16 TCSPC.msr: [testng] [2024-03-14 17:14:07,786] [pool-1-thread-8] Initializing /data/qa-7658/Document1_13-09-25.msr: [testng] [2024-03-14 17:14:07,993] [pool-1-thread-2] Initializing /data/paul/msr files - Paul Thomas UEA/Lifetime file.msr: [testng] [2024-03-14 17:14:08,218] [pool-1-thread-12] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_z-stack_FLIM_TDC_C0.ome.tif: [testng] [2024-03-14 17:14:08,847] [pool-1-thread-10] Initializing /data/qa-17102/2 channels FLIM z stack.msr: [testng] [2024-03-14 17:14:09,291] [pool-1-thread-4] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning.msr: [testng] [2024-03-14 17:14:09,620] [pool-1-thread-11] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel Zstack.msr: [testng] [2024-03-14 17:14:11,567] [pool-1-thread-2] Initializing /data/qa-17102/1 channel binning 8 time series.msr: [testng] [2024-03-14 17:14:11,835] [pool-1-thread-6] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel single slice.msr: [testng] [2024-03-14 17:14:12,025] [pool-1-thread-9] Initializing /data/qa-17102/2 channels FLIM time series.msr: [testng] [2024-03-14 17:14:12,235] [pool-1-thread-5] Initializing /data/qa-11369/01 - 770nm FITC - HybridPMT.msr: [testng] [2024-03-14 17:14:12,424] [pool-1-thread-8] Initializing /data/qa-27309/181109_e3_cut.msr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1484, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 41 seconds Finished: SUCCESS