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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@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins13435785715632040704.sh + '[' imaris = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_12882_merge_ci -v /uod/idr/repos/curated/imaris:/data -v /uod/idr-scratch/merge-ci/curated/imaris:/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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 09:47:24,404 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 09:47:24,405 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 09:47:24,405 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:47:24,406 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:47:24,407 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 09:47:24,407 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 09:47:24,407 |-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] 09:47:24,407 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:47:24,408 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:47:24,408 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 09:47:24,409 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 09:47:24,409 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 09:47:24,562 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 09:47:24,562 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 09:47:24,586 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 09:47:24,586 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 09:47:24,592 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 09:47:24,592 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 09:47:24,593 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 09:47:24,593 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 09:47:24,593 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 09:47:24,594 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 09:47:24,594 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 186 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-06 09:47:24,602] [main] java.version = 21 [testng] 09:47:24,605 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 09:47:24,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:47:24,648 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-06_09-47-24.log] [testng] 09:47:24,649 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-06-06 09:47:24,650] [main] testng.directory = /data [testng] [2024-06-06 09:47:24,651] [main] testng.configDirectory = /config [testng] [2024-06-06 09:47:24,659] [main] testng.multiplier = 1.0 [testng] [2024-06-06 09:47:24,660] [main] testng.in-memory = false [testng] [2024-06-06 09:47:24,660] [main] testng.allow-missing = false [testng] [2024-06-06 09:47:24,660] [main] user.language = en [testng] [2024-06-06 09:47:24,660] [main] user.country = ${user.country} [testng] [2024-06-06 09:47:24,660] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-06 09:47:31,477] [main] ---------------------------------------- [testng] [2024-06-06 09:47:31,477] [main] Total files: 67 [testng] [2024-06-06 09:47:31,477] [main] Scan time: 6.817 s (101 ms/file) [testng] [2024-06-06 09:47:31,477] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-06 09:47:53,725] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0006.ims: [testng] 09:47:53,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 09:47:53,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:47:53,726 |-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_09-47-53.log] [testng] 09:47:53,727 |-INFO in ch.qos.logback.core.sift.SiftProcessor@648a0b85 - End of configuration. [testng] [2024-06-06 09:47:53,748] [pool-1-thread-12] Initializing /data/public/davemason/Convallaria_3C_3T_2x2grid_confocal.ims: [testng] 09:47:53,749 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 09:47:53,749 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:47:53,749 |-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_09-47-53.log] [testng] 09:47:53,750 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60c2e92c - End of configuration. [testng] [2024-06-06 09:47:53,793] [pool-1-thread-11] Initializing /data/jason/imaris_5_5_demoimages/SwimmingAlgae.ims: [testng] 09:47:53,794 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 09:47:53,794 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:47:53,795 |-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_09-47-53.log] [testng] 09:47:53,796 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b58b62e - End of configuration. [testng] [2024-06-06 09:47:53,871] [pool-1-thread-10] Initializing /data/generated/MF-2CH-Z-T.ims: [testng] 09:47:53,871 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 09:47:53,871 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:47:53,872 |-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_09-47-53.log] [testng] 09:47:53,872 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5eeb454b - End of configuration. [testng] [2024-06-06 09:47:53,886] [pool-1-thread-9] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal_deconvolved.ims: [testng] 09:47:53,887 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 09:47:53,887 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:47:53,888 |-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_09-47-53.log] [testng] 09:47:53,888 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42789927 - End of configuration. [testng] [2024-06-06 09:47:53,920] [pool-1-thread-8] Initializing /data/generated/10-31_E_t0013.ims: [testng] 09:47:53,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 09:47:53,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:47:53,922 |-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_09-47-53.log] [testng] 09:47:53,922 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39e28d0f - End of configuration. [testng] [2024-06-06 09:47:53,934] [pool-1-thread-7] Initializing /data/qa-17839/Fusion _Stack.ims: [testng] 09:47:53,934 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 09:47:53,934 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:47:53,935 |-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_09-47-53.log] [testng] 09:47:53,936 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ce32a39 - End of configuration. [testng] [2024-06-06 09:47:53,992] [pool-1-thread-6] Initializing /data/public/eliana/retina_large.ims: [testng] 09:47:53,993 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 09:47:53,993 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:47:53,994 |-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_09-47-53.log] [testng] 09:47:53,994 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65c478e6 - End of configuration. [testng] [2024-06-06 09:47:54,018] [pool-1-thread-5] Initializing /data/jason/imaris_5_5_demoimages/PtK2Cell.ims: [testng] 09:47:54,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 09:47:54,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:47:54,019 |-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_09-47-54.log] [testng] 09:47:54,020 |-INFO in ch.qos.logback.core.sift.SiftProcessor@355e645c - End of configuration. [testng] [2024-06-06 09:47:54,050] [pool-1-thread-4] Initializing /data/generated/10-31_E_t0010.ims: [testng] 09:47:54,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 09:47:54,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:47:54,051 |-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_09-47-54.log] [testng] 09:47:54,052 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f252e57 - End of configuration. [testng] [2024-06-06 09:47:54,063] [pool-1-thread-3] Initializing /data/generated/10-31_E_t0014.ims: [testng] 09:47:54,063 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 09:47:54,063 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:47:54,064 |-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_09-47-54.log] [testng] 09:47:54,064 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6013bfe9 - End of configuration. [testng] [2024-06-06 09:47:54,075] [pool-1-thread-2] Initializing /data/qa-17515/Organoid=1.ims: [testng] 09:47:54,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 09:47:54,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:47:54,076 |-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_09-47-54.log] [testng] 09:47:54,076 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3aa0d576 - End of configuration. [testng] [2024-06-06 09:47:55,850] [pool-1-thread-8] Initializing /data/jason/imaris_5_5_demoimages/retina.ims: [testng] [2024-06-06 09:47:55,892] [pool-1-thread-3] Initializing /data/chris/supMovie3.ims: [testng] [2024-06-06 09:47:55,925] [pool-1-thread-1] Initializing /data/niko/imaris-testfile_5x5x5.ims: [testng] [2024-06-06 09:47:55,940] [pool-1-thread-4] Initializing /data/qa-17522/2016-07-26_17.11.03_Sample Prefix_5P298C2_Protocol.ims: [testng] [2024-06-06 09:47:56,004] [pool-1-thread-10] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal.ims: [testng] [2024-06-06 09:47:56,033] [pool-1-thread-5] Initializing /data/oliver/Stack2_float32Bit.ims: [testng] [2024-06-06 09:47:56,079] [pool-1-thread-11] Initializing /data/generated/10-31_E_t0000.ims: [testng] [2024-06-06 09:47:56,415] [pool-1-thread-9] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal_IMS3.ims: [testng] [2024-06-06 09:47:56,468] [pool-1-thread-1] Initializing /data/qa-8019/wrong_num_dimensions.ims: [testng] [2024-06-06 09:47:56,671] [pool-1-thread-11] Initializing /data/jcb/fig 6B GFP-AP-2d.ims: [testng] [2024-06-06 09:47:57,243] [pool-1-thread-8] Initializing /data/public/davemason/Convallaria_3C_10T_confocal.ims: BUILD SUCCESSFUL Total time: 2 minutes 33 seconds Finished: SUCCESS