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Started by upstream project "BIOFORMATS-test-repo" build number 104 originally caused by: Started by upstream project "Trigger" build number 116 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins9706078094135318751.sh + '[' zip = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_16067_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 01:22:48,033 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:22:48,035 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 01:22:48,035 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:22:48,036 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:22:48,037 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:22:48,037 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:22:48,038 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:22:48,038 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:22:48,038 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:22:48,039 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:22:48,040 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:22:48,040 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:22:48,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:22:48,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:22:48,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:22:48,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:22:48,225 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:22:48,225 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:22:48,225 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:22:48,226 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:22:48,226 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 01:22:48,227 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 01:22:48,227 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 189 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-27 01:22:48,235] [main] java.version = 21 [testng] 01:22:48,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:22:48,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:48,281 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-27_01-22-48.log] [testng] 01:22:48,282 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-06-27 01:22:48,284] [main] testng.directory = /data [testng] [2024-06-27 01:22:48,284] [main] testng.configDirectory = /config [testng] [2024-06-27 01:22:48,293] [main] testng.multiplier = 1.0 [testng] [2024-06-27 01:22:48,293] [main] testng.in-memory = false [testng] [2024-06-27 01:22:48,293] [main] testng.allow-missing = false [testng] [2024-06-27 01:22:48,293] [main] user.language = en [testng] [2024-06-27 01:22:48,293] [main] user.country = ${user.country} [testng] [2024-06-27 01:22:48,294] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-27 01:22:48,670] [main] ---------------------------------------- [testng] [2024-06-27 01:22:48,670] [main] Total files: 22 [testng] [2024-06-27 01:22:48,670] [main] Scan time: 0.376 s (17 ms/file) [testng] [2024-06-27 01:22:48,671] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 22 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-27 01:23:41,044] [pool-1-thread-1] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip: [testng] 01:23:41,045 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:23:41,045 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:41,046 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-27_01-23-41.log] [testng] 01:23:41,047 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38f0bb84 - End of configuration. [testng] [2024-06-27 01:23:42,550] [pool-1-thread-12] Initializing /data/imagej/watershed-animation.zip: [testng] 01:23:42,551 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:23:42,551 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:42,552 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-27_01-23-42.log] [testng] 01:23:42,552 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f50f29e - End of configuration. [testng] [2024-06-27 01:23:42,773] [pool-1-thread-11] Initializing /data/imagej/cheetah_256_8.tif.zip: [testng] 01:23:42,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:23:42,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:42,775 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-27_01-23-42.log] [testng] 01:23:42,775 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b196d81 - End of configuration. [testng] [2024-06-27 01:23:42,985] [pool-1-thread-10] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip: [testng] 01:23:42,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:23:42,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:42,986 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-27_01-23-42.log] [testng] 01:23:42,987 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14f2953c - End of configuration. [testng] [2024-06-27 01:23:44,498] [pool-1-thread-9] Initializing /data/imagej/mri-stack.zip: [testng] 01:23:44,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:23:44,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:44,499 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-27_01-23-44.log] [testng] 01:23:44,499 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e3e2091 - End of configuration. [testng] [2024-06-27 01:23:44,840] [pool-1-thread-8] Initializing /data/imagej/gel-electrophoresis.zip: [testng] 01:23:44,841 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:23:44,841 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:44,842 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-27_01-23-44.log] [testng] 01:23:44,842 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15042d07 - End of configuration. [testng] [2024-06-27 01:23:47,082] [pool-1-thread-7] Initializing /data/imagej/3D_Chromosome.zip: [testng] 01:23:47,082 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:23:47,082 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:47,083 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-27_01-23-47.log] [testng] 01:23:47,083 |-INFO in ch.qos.logback.core.sift.SiftProcessor@260903aa - End of configuration. [testng] [2024-06-27 01:23:47,549] [pool-1-thread-6] Initializing /data/imagej/hela-cells.zip: [testng] 01:23:47,550 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:23:47,550 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:47,550 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-27_01-23-47.log] [testng] 01:23:47,551 |-INFO in ch.qos.logback.core.sift.SiftProcessor@629fa43d - End of configuration. [testng] [2024-06-27 01:23:48,569] [pool-1-thread-5] Initializing /data/imagej/FluorescentCells.zip: [testng] 01:23:48,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:23:48,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:48,570 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-27_01-23-48.log] [testng] 01:23:48,571 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a10c7ca - End of configuration. [testng] [2024-06-27 01:23:48,829] [pool-1-thread-4] Initializing /data/imagej/flybrain.zip: [testng] 01:23:48,830 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:23:48,830 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:48,831 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-27_01-23-48.log] [testng] 01:23:48,832 |-INFO in ch.qos.logback.core.sift.SiftProcessor@148c9c87 - End of configuration. [testng] [2024-06-27 01:23:55,213] [pool-1-thread-3] Initializing /data/imagej/4D-Stack(256x256x20x10).zip: [testng] 01:23:55,214 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:23:55,214 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:55,215 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-27_01-23-55.log] [testng] 01:23:55,215 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27c23bfe - End of configuration. [testng] [2024-06-27 01:24:02,380] [pool-1-thread-2] Initializing /data/imagej/xrays.zip: [testng] 01:24:02,380 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:24:02,380 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:02,381 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-27_01-24-02.log] [testng] 01:24:02,382 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3424afd6 - End of configuration. [testng] [2024-06-27 01:24:05,346] [pool-1-thread-2] Initializing /data/imagej/confocal-series.zip: [testng] [2024-06-27 01:24:11,537] [pool-1-thread-11] Initializing /data/samples/bat-cochlea-volume.zip: [testng] [2024-06-27 01:24:14,231] [pool-1-thread-12] Initializing /data/imagej/RatBrain.zip: [testng] [2024-06-27 01:24:14,992] [pool-1-thread-5] Initializing /data/imagej/confocal-stack.zip: [testng] [2024-06-27 01:24:24,949] [pool-1-thread-9] Initializing /data/imagej/scala-media.zip: [testng] [2024-06-27 01:24:25,580] [pool-1-thread-7] Initializing /data/imagej/m51.zip: [testng] [2024-06-27 01:24:26,582] [pool-1-thread-12] Initializing /data/imagej/blood-brain-barrier.zip: [testng] [2024-06-27 01:24:33,118] [pool-1-thread-9] Initializing /data/imagej/se3.zip: [testng] [2024-06-27 01:24:39,524] [pool-1-thread-7] Initializing /data/samples/sdub.zip: [testng] [2024-06-27 01:24:46,453] [pool-1-thread-6] Initializing /data/imagej/fat-cells.zip: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1166, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 7 minutes 11 seconds Finished: SUCCESS