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Started by upstream project "BIOFORMATS-test-repo" build number 6 originally caused by: Started by upstream project "Trigger" build number 9 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins14133991731701481017.sh + '[' zip = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_812_merge_ci -v /uod/idr/repos/curated/zip:/data -v /uod/idr-scratch/merge-ci/curated/zip:/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] 1 warning 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] 09:42:01,755 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 09:42:01,756 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 09:42:01,756 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:42:01,757 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:42:01,757 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 09:42:01,758 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 09:42:01,758 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 09:42:01,758 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:42:01,758 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:42:01,759 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 09:42:01,759 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 09:42:01,760 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 09:42:01,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 09:42:01,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 09:42:01,939 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 09:42:01,939 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 09:42:01,945 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 09:42:01,945 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 09:42:01,945 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 09:42:01,945 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 09:42:01,945 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 09:42:01,946 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 09:42:01,947 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 189 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-20 09:42:01,955] [main] java.version = 17.0.2 [testng] 09:42:01,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 09:42:01,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:42:01,998 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-20_09-42-01.log] [testng] 09:42:02,000 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-03-20 09:42:02,001] [main] testng.directory = /data [testng] [2024-03-20 09:42:02,002] [main] testng.configDirectory = /config [testng] [2024-03-20 09:42:02,010] [main] testng.multiplier = 1.0 [testng] [2024-03-20 09:42:02,011] [main] testng.in-memory = false [testng] [2024-03-20 09:42:02,011] [main] testng.allow-missing = false [testng] [2024-03-20 09:42:02,011] [main] user.language = en [testng] [2024-03-20 09:42:02,011] [main] user.country = ${user.country} [testng] [2024-03-20 09:42:02,011] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-20 09:42:02,359] [main] ---------------------------------------- [testng] [2024-03-20 09:42:02,359] [main] Total files: 22 [testng] [2024-03-20 09:42:02,359] [main] Scan time: 0.348 s (15 ms/file) [testng] [2024-03-20 09:42:02,359] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-20 09:43:07,847] [pool-1-thread-1] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] 09:43:07,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 09:43:07,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:43:07,848 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-20_09-43-07.log] [testng] 09:43:07,849 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60e29e1c - End of configuration. [testng] [2024-03-20 09:43:13,902] [pool-1-thread-12] Initializing /data/imagej/fat-cells.zip: [testng] 09:43:13,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 09:43:13,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:43:13,903 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-20_09-43-13.log] [testng] 09:43:13,904 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2858bf4a - End of configuration. [testng] [2024-03-20 09:43:16,561] [pool-1-thread-11] Initializing /data/imagej/FluorescentCells.zip: [testng] 09:43:16,561 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 09:43:16,561 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:43:16,562 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-20_09-43-16.log] [testng] 09:43:16,562 |-INFO in ch.qos.logback.core.sift.SiftProcessor@16b70496 - End of configuration. [testng] [2024-03-20 09:43:17,273] [pool-1-thread-10] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] 09:43:17,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 09:43:17,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:43:17,274 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-20_09-43-17.log] [testng] 09:43:17,274 |-INFO in ch.qos.logback.core.sift.SiftProcessor@553f1812 - End of configuration. [testng] [2024-03-20 09:43:18,748] [pool-1-thread-9] Initializing /data/imagej/xrays.zip: [testng] 09:43:18,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 09:43:18,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:43:18,749 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-20_09-43-18.log] [testng] 09:43:18,749 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59dea1af - End of configuration. [testng] [2024-03-20 09:43:19,149] [pool-1-thread-8] Initializing /data/imagej/confocal-series.zip: [testng] 09:43:19,150 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 09:43:19,150 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:43:19,150 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-20_09-43-19.log] [testng] 09:43:19,151 |-INFO in ch.qos.logback.core.sift.SiftProcessor@378dfbbd - End of configuration. [testng] [2024-03-20 09:43:23,382] [pool-1-thread-7] Initializing /data/imagej/watershed-animation.zip: [testng] 09:43:23,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 09:43:23,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:43:23,383 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-20_09-43-23.log] [testng] 09:43:23,384 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bd11776 - End of configuration. [testng] [2024-03-20 09:43:24,024] [pool-1-thread-6] Initializing /data/imagej/scala-media.zip: [testng] 09:43:24,024 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 09:43:24,024 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:43:24,025 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-20_09-43-24.log] [testng] 09:43:24,025 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75084d66 - End of configuration. [testng] [2024-03-20 09:43:24,618] [pool-1-thread-5] Initializing /data/imagej/m51.zip: [testng] 09:43:24,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 09:43:24,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:43:24,619 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-20_09-43-24.log] [testng] 09:43:24,620 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35027bb6 - End of configuration. [testng] [2024-03-20 09:43:25,263] [pool-1-thread-4] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] 09:43:25,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 09:43:25,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:43:25,264 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-20_09-43-25.log] [testng] 09:43:25,264 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28a94273 - End of configuration. [testng] [2024-03-20 09:43:27,109] [pool-1-thread-3] Initializing /data/imagej/hela-cells.zip: [testng] 09:43:27,109 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 09:43:27,109 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:43:27,109 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-20_09-43-27.log] [testng] 09:43:27,110 |-INFO in ch.qos.logback.core.sift.SiftProcessor@949af37 - End of configuration. [testng] [2024-03-20 09:43:28,367] [pool-1-thread-2] Initializing /data/samples/bat-cochlea-volume.zip: [testng] 09:43:28,367 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 09:43:28,367 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:43:28,368 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-20_09-43-28.log] [testng] 09:43:28,368 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a0069cd - End of configuration. [testng] [2024-03-20 09:43:35,542] [pool-1-thread-9] Initializing /data/imagej/RatBrain.zip: [testng] [2024-03-20 09:43:36,309] [pool-1-thread-6] Initializing /data/imagej/flybrain.zip: [testng] [2024-03-20 09:43:41,620] [pool-1-thread-5] Initializing /data/imagej/3D_Chromosome.zip: [testng] [2024-03-20 09:43:43,633] [pool-1-thread-7] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] [2024-03-20 09:43:46,271] [pool-1-thread-11] Initializing /data/imagej/gel-electrophoresis.zip: [testng] [2024-03-20 09:43:49,946] [pool-1-thread-9] Initializing /data/imagej/se3.zip: [testng] [2024-03-20 09:43:56,517] [pool-1-thread-7] Initializing /data/samples/sdub.zip: [testng] [2024-03-20 09:43:59,918] [pool-1-thread-5] Initializing /data/imagej/blood-brain-barrier.zip: [testng] [2024-03-20 09:44:05,038] [pool-1-thread-2] Initializing /data/imagej/mri-stack.zip: [testng] [2024-03-20 09:44:07,294] [pool-1-thread-3] Initializing /data/imagej/confocal-stack.zip: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1166, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 6 minutes 23 seconds Finished: SUCCESS