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Started by upstream project "BIOFORMATS-test-repo" build number 386 originally caused by: Started by upstream project "Trigger" build number 408 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@18 [BIOFORMATS-test-folder@18] $ /bin/bash -xe /tmp/jenkins12588927697210395693.sh + '[' imspector = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_61114_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] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-mdbtools/5.3.4-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/metakit/5.8.9-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-poi/5.3.10-SNAPSHOT/maven-metadata.xml [resolver:resolve] Resolving artifacts [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-mdbtools/5.3.4-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/metakit/5.8.9-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-poi/5.3.10-SNAPSHOT/maven-metadata.xml compile-tests: [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-mdbtools/5.3.4-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/metakit/5.8.9-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-poi/5.3.10-SNAPSHOT/maven-metadata.xml [resolver:resolve] Resolving artifacts [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-mdbtools/5.3.4-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/metakit/5.8.9-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-poi/5.3.10-SNAPSHOT/maven-metadata.xml [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] 00:30:49,833 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:30:49,834 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - No custom configurators were discovered as a service. [testng] 00:30:49,834 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:30:49,835 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:30:49,836 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:30:49,836 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:30:49,836 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:30:49,836 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:30:49,837 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:30:49,837 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:30:49,838 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:30:49,838 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:30:49,988 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:30:49,988 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:30:50,012 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:30:50,012 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:30:50,019 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:30:50,019 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:30:50,019 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:30:50,019 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:30:50,019 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@4310d43 - End of configuration. [testng] 00:30:50,020 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@1b11171f - Registering current configuration as safe fallback point [testng] 00:30:50,020 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 183 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-21 00:30:50,029] [main] java.version = 21 [testng] 00:30:50,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:30:50,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:50,073 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-21_00-30-50.log] [testng] 00:30:50,074 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69504ae9 - End of configuration. [testng] [2025-03-21 00:30:50,076] [main] testng.directory = /data [testng] [2025-03-21 00:30:50,076] [main] testng.configDirectory = /config [testng] [2025-03-21 00:30:50,084] [main] testng.multiplier = 1.0 [testng] [2025-03-21 00:30:50,085] [main] testng.in-memory = false [testng] [2025-03-21 00:30:50,085] [main] testng.allow-missing = false [testng] [2025-03-21 00:30:50,085] [main] user.language = en [testng] [2025-03-21 00:30:50,085] [main] user.country = ${user.country} [testng] [2025-03-21 00:30:50,085] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-21 00:32:05,127] [main] ---------------------------------------- [testng] [2025-03-21 00:32:05,127] [main] Total files: 31 [testng] [2025-03-21 00:32:05,127] [main] Scan time: 75.042 s (2420 ms/file) [testng] [2025-03-21 00:32:05,127] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 29 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-21 00:33:55,084] [pool-1-thread-1] Initializing /data/qa-7936/z-TC - for LOCI.msr: [testng] 00:33:55,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:33:55,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:55,086 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-21_00-33-55.log] [testng] 00:33:55,086 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12b47397 - End of configuration. [testng] [2025-03-21 00:33:57,970] [pool-1-thread-12] Initializing /data/qa-4929/OMERO data/01 - 27hpf_f2-GFP-wt1b+rfp-flk1 - 3channel-z-stack.msr: [testng] 00:33:57,970 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:33:57,970 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:57,971 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-21_00-33-57.log] [testng] 00:33:57,971 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67628b32 - End of configuration. [testng] [2025-03-21 00:34:00,899] [pool-1-thread-11] Initializing /data/qa-7992/ArrayIndexOutOfBoundsException.msr: [testng] 00:34:00,899 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:34:00,899 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:00,900 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-21_00-34-00.log] [testng] 00:34:00,900 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e667db3 - End of configuration. [testng] [2025-03-21 00:34:03,705] [pool-1-thread-10] Initializing /data/qa-7658/Document1_13-09-25.msr: [testng] 00:34:03,705 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:34:03,705 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:03,706 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-21_00-34-03.log] [testng] 00:34:03,706 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f731d9e - End of configuration. [testng] [2025-03-21 00:34:07,094] [pool-1-thread-9] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning.msr: [testng] 00:34:07,095 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:34:07,095 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:07,095 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-21_00-34-07.log] [testng] 00:34:07,096 |-INFO in ch.qos.logback.core.sift.SiftProcessor@124acfe5 - End of configuration. [testng] [2025-03-21 00:34:10,469] [pool-1-thread-8] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel single slice 4 tiles.msr: [testng] 00:34:10,469 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:34:10,469 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:10,470 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-21_00-34-10.log] [testng] 00:34:10,470 |-INFO in ch.qos.logback.core.sift.SiftProcessor@109f3fbb - End of configuration. [testng] [2025-03-21 00:34:13,267] [pool-1-thread-7] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel single slice.msr: [testng] 00:34:13,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:34:13,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:13,268 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-21_00-34-13.log] [testng] 00:34:13,269 |-INFO in ch.qos.logback.core.sift.SiftProcessor@529be425 - End of configuration. [testng] [2025-03-21 00:34:15,957] [pool-1-thread-6] Initializing /data/qa-17102/1 channel binning 8 time series.msr: [testng] 00:34:15,957 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:34:15,957 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:15,958 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-21_00-34-15.log] [testng] 00:34:15,958 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f489524 - End of configuration. [testng] [2025-03-21 00:34:19,204] [pool-1-thread-5] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel Zstack.msr: [testng] 00:34:19,204 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:34:19,204 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:19,205 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-21_00-34-19.log] [testng] 00:34:19,205 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e00f3cb - End of configuration. [testng] [2025-03-21 00:34:22,222] [pool-1-thread-4] Initializing /data/qa-9468/HPDR10467U-40-VD0191-red-100pc-without-tube.msr: [testng] 00:34:22,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:34:22,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:22,222 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-21_00-34-22.log] [testng] 00:34:22,223 |-INFO in ch.qos.logback.core.sift.SiftProcessor@640fd262 - End of configuration. [testng] [2025-03-21 00:34:24,908] [pool-1-thread-3] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_z-stack_FLIM_TDC_C0.ome.tif: [testng] 00:34:24,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:34:24,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:24,908 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-21_00-34-24.log] [testng] 00:34:24,909 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d059742 - End of configuration. [testng] [2025-03-21 00:34:28,915] [pool-1-thread-2] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel Zstack.msr: [testng] 00:34:28,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:34:28,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:28,916 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-21_00-34-28.log] [testng] 00:34:28,916 |-INFO in ch.qos.logback.core.sift.SiftProcessor@96d371b - End of configuration. [testng] [2025-03-21 00:34:45,927] [pool-1-thread-7] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_FLIM_z-stack_1.msr: [testng] [2025-03-21 00:34:48,018] [pool-1-thread-6] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning_12-08-53_TCSPC_C0.ome.tif: [testng] [2025-03-21 00:34:51,992] [pool-1-thread-11] Initializing /data/qa-7992/NegativeArraySizeException_small.msr: [testng] [2025-03-21 00:34:54,381] [pool-1-thread-10] Initializing /data/qa-17102/2 channels FLIM time series.msr: [testng] [2025-03-21 00:34:56,834] [pool-1-thread-12] Initializing /data/qa-7992/IllegalArgumentException.msr: [testng] [2025-03-21 00:34:59,415] [pool-1-thread-1] Initializing /data/qa-7936/02 - not working.msr: [testng] [2025-03-21 00:35:01,988] [pool-1-thread-4] Initializing /data/qa-11369/01 - 770nm FITC - HybridPMT.msr: [testng] [2025-03-21 00:35:04,697] [pool-1-thread-2] Initializing /data/qa-4929/OMERO data/01 - urea_irf_image_TCSPC-data.msr: [testng] [2025-03-21 00:35:07,778] [pool-1-thread-5] Initializing /data/qa-17102/1 channel binning 4 time series.msr: [testng] [2025-03-21 00:35:10,755] [pool-1-thread-8] Initializing /data/public/zenodo-10476252/test.msr: [testng] [2025-03-21 00:35:13,688] [pool-1-thread-9] Initializing /data/qa-17102/2 channels FLIM z stack.msr: [testng] [2025-03-21 00:35:17,199] [pool-1-thread-3] Initializing /data/qa-7936/01 - working.msr: [testng] [2025-03-21 00:35:36,611] [pool-1-thread-7] Initializing /data/qa-11369/02 - 70 - 1 - tp1 - x16 TCSPC.msr: [testng] [2025-03-21 00:35:39,440] [pool-1-thread-11] 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] [2025-03-21 00:35:52,269] [pool-1-thread-10] Initializing /data/qa-27309/181109_e3_cut.msr: [testng] [2025-03-21 00:35:54,930] [pool-1-thread-2] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps.msr: [testng] [2025-03-21 00:35:57,612] [pool-1-thread-5] Initializing /data/paul/msr files - Paul Thomas UEA/Lifetime file.msr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1537, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 6 minutes 50 seconds Finished: SUCCESS