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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@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins731691851802399779.sh + '[' pcx = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_3_merge_ci -v /uod/idr/repos/curated/pcx:/data -v /uod/idr-scratch/devspace/curated/pcx:/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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 15:58:24,949 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 15:58:24,951 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 15:58:24,951 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 15:58:24,952 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 15:58:24,952 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 15:58:24,953 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 15:58:24,953 |-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] 15:58:24,953 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 15:58:24,954 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 15:58:24,954 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 15:58:24,954 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 15:58:24,955 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 15:58:25,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 15:58:25,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 15:58:25,131 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 15:58:25,131 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 15:58:25,138 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 15:58:25,138 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 15:58:25,138 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 15:58:25,138 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 15:58:25,138 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 15:58:25,139 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 15:58:25,139 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 185 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-14 15:58:25,147] [main] java.version = 21 [testng] 15:58:25,150 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 15:58:25,150 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:58:25,198 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-14_15-58-25.log] [testng] 15:58:25,199 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-03-14 15:58:25,201] [main] testng.directory = /data [testng] [2024-03-14 15:58:25,201] [main] testng.configDirectory = /config [testng] [2024-03-14 15:58:25,210] [main] testng.multiplier = 1.0 [testng] [2024-03-14 15:58:25,210] [main] testng.in-memory = false [testng] [2024-03-14 15:58:25,210] [main] testng.allow-missing = false [testng] [2024-03-14 15:58:25,210] [main] user.language = en [testng] [2024-03-14 15:58:25,210] [main] user.country = ${user.country} [testng] [2024-03-14 15:58:25,210] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-14 15:58:25,680] [main] ---------------------------------------- [testng] [2024-03-14 15:58:25,680] [main] Total files: 36 [testng] [2024-03-14 15:58:25,680] [main] Scan time: 0.469 s (13 ms/file) [testng] [2024-03-14 15:58:25,680] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 35 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-14 15:58:26,861] [pool-1-thread-1] Initializing /data/generated/mri-stack17.pcx: [testng] 15:58:26,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 15:58:26,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:58:26,863 |-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_15-58-26.log] [testng] 15:58:26,863 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ed4ea05 - End of configuration. [testng] [2024-03-14 15:58:26,875] [pool-1-thread-12] Initializing /data/generated/mri-stack15.pcx: [testng] 15:58:26,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 15:58:26,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:58:26,876 |-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_15-58-26.log] [testng] 15:58:26,876 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b60ca87 - End of configuration. [testng] [2024-03-14 15:58:26,882] [pool-1-thread-11] Initializing /data/generated/mri-stack18.pcx: [testng] 15:58:26,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 15:58:26,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:58:26,883 |-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_15-58-26.log] [testng] 15:58:26,884 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7dc0ef37 - End of configuration. [testng] [2024-03-14 15:58:26,889] [pool-1-thread-10] Initializing /data/generated/mri-stack20.pcx: [testng] 15:58:26,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 15:58:26,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:58:26,890 |-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_15-58-26.log] [testng] 15:58:26,891 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ab58e56 - End of configuration. [testng] [2024-03-14 15:58:26,902] [pool-1-thread-9] Initializing /data/josh/Screenshots/deltavision.pcx: [testng] 15:58:26,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 15:58:26,903 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:58:26,903 |-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_15-58-26.log] [testng] 15:58:26,904 |-INFO in ch.qos.logback.core.sift.SiftProcessor@505501df - End of configuration. [testng] [2024-03-14 15:58:26,914] [pool-1-thread-8] Initializing /data/generated/mri-stack5.pcx: [testng] 15:58:26,914 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 15:58:26,914 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:58:26,915 |-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_15-58-26.log] [testng] 15:58:26,916 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a33754 - End of configuration. [testng] [2024-03-14 15:58:26,921] [pool-1-thread-7] Initializing /data/josh/Screenshots/fv1000color.pcx: [testng] 15:58:26,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 15:58:26,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:58:26,921 |-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_15-58-26.log] [testng] 15:58:26,922 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b2a2f3a - End of configuration. [testng] [2024-03-14 15:58:26,931] [pool-1-thread-6] Initializing /data/generated/mri-stack13.pcx: [testng] 15:58:26,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 15:58:26,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:58:26,931 |-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_15-58-26.log] [testng] 15:58:26,932 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2032d1e9 - End of configuration. [testng] [2024-03-14 15:58:26,937] [pool-1-thread-5] Initializing /data/generated/mri-stack7.pcx: [testng] 15:58:26,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 15:58:26,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:58:26,938 |-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_15-58-26.log] [testng] 15:58:26,938 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f823a69 - End of configuration. [testng] [2024-03-14 15:58:26,943] [pool-1-thread-4] Initializing /data/generated/mri-stack21.pcx: [testng] 15:58:26,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 15:58:26,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:58:26,944 |-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_15-58-26.log] [testng] 15:58:26,944 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6831edeb - End of configuration. [testng] [2024-03-14 15:58:26,949] [pool-1-thread-3] Initializing /data/generated/mri-stack12.pcx: [testng] 15:58:26,949 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 15:58:26,949 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:58:26,949 |-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_15-58-26.log] [testng] 15:58:26,950 |-INFO in ch.qos.logback.core.sift.SiftProcessor@576ccf87 - End of configuration. [testng] [2024-03-14 15:58:26,955] [pool-1-thread-2] Initializing /data/generated/mri-stack11.pcx: [testng] 15:58:26,955 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 15:58:26,955 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:58:26,956 |-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_15-58-26.log] [testng] 15:58:26,956 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e20cdd - End of configuration. [testng] [2024-03-14 15:58:29,032] [pool-1-thread-3] Initializing /data/generated/mri-stack22.pcx: [testng] [2024-03-14 15:58:29,037] [pool-1-thread-8] Initializing /data/generated/mri-stack26.pcx: [testng] [2024-03-14 15:58:29,042] [pool-1-thread-10] Initializing /data/generated/mri-stack3.pcx: [testng] [2024-03-14 15:58:29,048] [pool-1-thread-4] Initializing /data/generated/mri-stack19.pcx: [testng] [2024-03-14 15:58:29,053] [pool-1-thread-2] Initializing /data/josh/Screenshots/Metamorph image-stack.pcx: [testng] [2024-03-14 15:58:29,061] [pool-1-thread-1] Initializing /data/generated/mri-stack9.pcx: [testng] [2024-03-14 15:58:29,068] [pool-1-thread-5] Initializing /data/generated/mri-stack25.pcx: [testng] [2024-03-14 15:58:29,076] [pool-1-thread-11] Initializing /data/generated/mri-stack10.pcx: [testng] [2024-03-14 15:58:29,081] [pool-1-thread-6] Initializing /data/josh/Screenshots/nd2 color.pcx: [testng] [2024-03-14 15:58:29,089] [pool-1-thread-12] Initializing /data/generated/mri-stack23.pcx: [testng] [2024-03-14 15:58:29,094] [pool-1-thread-9] Initializing /data/generated/mri-stack14.pcx: [testng] [2024-03-14 15:58:29,099] [pool-1-thread-7] Initializing /data/josh/Screenshots/slidebooksamezposition.pcx: [testng] [2024-03-14 15:58:29,446] [pool-1-thread-8] Initializing /data/josh/Screenshots/leica-lif.pcx: [testng] [2024-03-14 15:58:29,471] [pool-1-thread-1] Initializing /data/josh/Screenshots/biorad color off.pcx: [testng] [2024-03-14 15:58:29,478] [pool-1-thread-4] Initializing /data/generated/mri-stack2.pcx: [testng] [2024-03-14 15:58:29,502] [pool-1-thread-5] Initializing /data/generated/mri-stack8.pcx: [testng] [2024-03-14 15:58:29,507] [pool-1-thread-10] Initializing /data/generated/mri-stack1.pcx: [testng] [2024-03-14 15:58:29,550] [pool-1-thread-12] Initializing /data/generated/mri-stack0.pcx: [testng] [2024-03-14 15:58:29,558] [pool-1-thread-9] Initializing /data/generated/mri-stack16.pcx: [testng] [2024-03-14 15:58:29,564] [pool-1-thread-3] Initializing /data/josh/Screenshots/epscolor.pcx: [testng] [2024-03-14 15:58:29,571] [pool-1-thread-11] Initializing /data/generated/mri-stack4.pcx: [testng] [2024-03-14 15:58:29,708] [pool-1-thread-4] Initializing /data/generated/mri-stack24.pcx: [testng] [2024-03-14 15:58:29,728] [pool-1-thread-5] Initializing /data/generated/mri-stack6.pcx: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1855, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 7 seconds Finished: SUCCESS