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Started by upstream project "BIOFORMATS-test-repo" build number 284 originally caused by: Started by upstream project "Trigger" build number 303 originally caused by: Started by timer 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/jenkins7878384995762788013.sh + '[' zip = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_44787_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] 00:26:41,150 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:26:41,151 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:26:41,151 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:26:41,152 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:26:41,153 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:26:41,153 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:26:41,154 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:26:41,154 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:26:41,154 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:26:41,155 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:26:41,155 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:26:41,156 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:26:41,410 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:26:41,410 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:26:41,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:26:41,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:26:41,437 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:26:41,437 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:26:41,437 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:26:41,437 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:26:41,437 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:26:41,438 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:26:41,438 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 284 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-08 00:26:41,447] [main] java.version = 17.0.2 [testng] 00:26:41,465 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:26:41,465 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:26:41,505 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-08_00-26-41.log] [testng] 00:26:41,506 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-12-08 00:26:41,508] [main] testng.directory = /data [testng] [2024-12-08 00:26:41,508] [main] testng.configDirectory = /config [testng] [2024-12-08 00:26:41,517] [main] testng.multiplier = 1.0 [testng] [2024-12-08 00:26:41,517] [main] testng.in-memory = false [testng] [2024-12-08 00:26:41,517] [main] testng.allow-missing = false [testng] [2024-12-08 00:26:41,518] [main] user.language = en [testng] [2024-12-08 00:26:41,518] [main] user.country = ${user.country} [testng] [2024-12-08 00:26:41,518] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-08 00:26:42,371] [main] ---------------------------------------- [testng] [2024-12-08 00:26:42,371] [main] Total files: 22 [testng] [2024-12-08 00:26:42,371] [main] Scan time: 0.853 s (38 ms/file) [testng] [2024-12-08 00:26:42,372] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-08 00:28:57,070] [pool-1-thread-1] Initializing /data/imagej/fat-cells.zip: [testng] 00:28:57,070 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:28:57,070 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:28:57,071 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-08_00-28-57.log] [testng] 00:28:57,072 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21177b01 - End of configuration. [testng] [2024-12-08 00:29:01,697] [pool-1-thread-12] Initializing /data/imagej/gel-electrophoresis.zip: [testng] 00:29:01,697 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:29:01,697 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:01,698 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-08_00-29-01.log] [testng] 00:29:01,699 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12e898bc - End of configuration. [testng] [2024-12-08 00:29:06,586] [pool-1-thread-11] Initializing /data/imagej/3D_Chromosome.zip: [testng] 00:29:06,586 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:29:06,586 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:06,587 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-08_00-29-06.log] [testng] 00:29:06,587 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35dffa3d - End of configuration. [testng] [2024-12-08 00:29:10,002] [pool-1-thread-10] Initializing /data/imagej/xrays.zip: [testng] 00:29:10,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:29:10,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:10,003 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-08_00-29-10.log] [testng] 00:29:10,003 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35d0197e - End of configuration. [testng] [2024-12-08 00:29:12,350] [pool-1-thread-9] Initializing /data/imagej/flybrain.zip: [testng] 00:29:12,351 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:29:12,351 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:12,351 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-08_00-29-12.log] [testng] 00:29:12,352 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b8d9f03 - End of configuration. [testng] [2024-12-08 00:29:22,497] [pool-1-thread-8] Initializing /data/imagej/m51.zip: [testng] 00:29:22,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:29:22,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:22,498 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-08_00-29-22.log] [testng] 00:29:22,498 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4fa3eb9b - End of configuration. [testng] [2024-12-08 00:29:24,467] [pool-1-thread-7] Initializing /data/imagej/se3.zip: [testng] 00:29:24,467 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:29:24,467 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:24,468 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-08_00-29-24.log] [testng] 00:29:24,468 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39d07b87 - End of configuration. [testng] [2024-12-08 00:29:32,766] [pool-1-thread-6] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] 00:29:32,766 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:29:32,766 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:32,768 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-08_00-29-32.log] [testng] 00:29:32,768 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65af82f8 - End of configuration. [testng] [2024-12-08 00:29:36,295] [pool-1-thread-5] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] 00:29:36,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:29:36,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:36,297 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-08_00-29-36.log] [testng] 00:29:36,298 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bbd8a9e - End of configuration. [testng] [2024-12-08 00:29:41,190] [pool-1-thread-4] Initializing /data/imagej/RatBrain.zip: [testng] 00:29:41,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:29:41,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:41,192 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-08_00-29-41.log] [testng] 00:29:41,192 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a87b0b0 - End of configuration. [testng] [2024-12-08 00:29:45,543] [pool-1-thread-3] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] 00:29:45,543 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:29:45,543 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:45,544 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-08_00-29-45.log] [testng] 00:29:45,544 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47b92663 - End of configuration. [testng] [2024-12-08 00:29:55,996] [pool-1-thread-2] Initializing /data/imagej/hela-cells.zip: [testng] 00:29:55,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:29:55,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:55,997 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-08_00-29-55.log] [testng] 00:29:55,998 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10033bd5 - End of configuration. [testng] [2024-12-08 00:30:36,030] [pool-1-thread-10] Initializing /data/samples/bat-cochlea-volume.zip: [testng] [2024-12-08 00:30:41,226] [pool-1-thread-8] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] [2024-12-08 00:30:49,940] [pool-1-thread-4] Initializing /data/imagej/confocal-stack.zip: [testng] [2024-12-08 00:31:03,918] [pool-1-thread-11] Initializing /data/imagej/scala-media.zip: [testng] [2024-12-08 00:31:06,965] [pool-1-thread-6] Initializing /data/samples/sdub.zip: [testng] [2024-12-08 00:31:25,193] [pool-1-thread-6] Initializing /data/imagej/mri-stack.zip: [testng] [2024-12-08 00:31:31,714] [pool-1-thread-2] Initializing /data/imagej/blood-brain-barrier.zip: [testng] [2024-12-08 00:31:51,572] [pool-1-thread-12] Initializing /data/imagej/watershed-animation.zip: [testng] [2024-12-08 00:31:54,514] [pool-1-thread-5] Initializing /data/imagej/FluorescentCells.zip: [testng] [2024-12-08 00:31:58,708] [pool-1-thread-11] Initializing /data/imagej/confocal-series.zip: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1166, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 9 minutes 9 seconds Finished: SUCCESS