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Started by upstream project "BIOFORMATS-test-repo" build number 42 originally caused by: Started by upstream project "Trigger" build number 49 originally caused by: Started by user devspace 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/jenkins3616378730279898048.sh + '[' micromanager = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_5964_merge_ci -v /uod/idr/repos/curated/micromanager:/data -v /uod/idr-scratch/merge-ci/curated/micromanager:/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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 06:53:41,234 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 06:53:41,237 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 06:53:41,237 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:53:41,238 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:53:41,239 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 06:53:41,240 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 06:53:41,240 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 06:53:41,240 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:53:41,241 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:53:41,242 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 06:53:41,243 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 06:53:41,243 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 06:53:41,468 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 06:53:41,468 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 06:53:41,491 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 06:53:41,491 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 06:53:41,497 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 06:53:41,497 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 06:53:41,497 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 06:53:41,498 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 06:53:41,498 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 06:53:41,498 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 06:53:41,499 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 258 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-23 06:53:41,509] [main] java.version = 11.0.16 [testng] 06:53:41,512 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 06:53:41,512 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:53:41,566 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-23_06-53-41.log] [testng] 06:53:41,568 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-04-23 06:53:41,571] [main] testng.directory = /data [testng] [2024-04-23 06:53:41,571] [main] testng.configDirectory = /config [testng] [2024-04-23 06:53:41,584] [main] testng.multiplier = 1.0 [testng] [2024-04-23 06:53:41,586] [main] testng.in-memory = false [testng] [2024-04-23 06:53:41,586] [main] testng.allow-missing = false [testng] [2024-04-23 06:53:41,586] [main] user.language = en [testng] [2024-04-23 06:53:41,586] [main] user.country = ${user.country} [testng] [2024-04-23 06:53:41,586] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-04-23 06:53:51,631] [main] ---------------------------------------- [testng] [2024-04-23 06:53:51,631] [main] Total files: 1686 [testng] [2024-04-23 06:53:51,631] [main] Scan time: 10.045 s (5 ms/file) [testng] [2024-04-23 06:53:51,631] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 49 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-23 06:59:19,946] [pool-1-thread-1] Initializing /data/public/1.4.22/thomas/test/test_stack/test_stack_MMStack_Pos0_metadata.txt: [testng] 06:59:19,947 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 06:59:19,947 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:59:19,949 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-23_06-59-19.log] [testng] 06:59:19,950 |-INFO in ch.qos.logback.core.sift.SiftProcessor@615a37b6 - End of configuration. [testng] [2024-04-23 06:59:19,997] [pool-1-thread-12] Initializing /data/eric/GFP-Aladin mCh-Tub_5/Acqusition.xml: [testng] 06:59:19,997 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 06:59:19,997 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:59:19,998 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-23_06-59-19.log] [testng] 06:59:19,998 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ee6cd4a - End of configuration. [testng] [2024-04-23 06:59:20,918] [pool-1-thread-11] Initializing /data/public/1.4.22/sebastien/Test_Dataset_MultiPosition_Stack_1_MMStack_Pos0_metadata.txt: [testng] 06:59:20,919 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 06:59:20,919 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:59:20,920 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-23_06-59-20.log] [testng] 06:59:20,920 |-INFO in ch.qos.logback.core.sift.SiftProcessor@196ed87c - End of configuration. [testng] [2024-04-23 06:59:48,530] [pool-1-thread-10] Initializing /data/nico/test2/img_000000000_Cy5_000.tif: [testng] 06:59:48,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 06:59:48,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:59:48,531 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-23_06-59-48.log] [testng] 06:59:48,532 |-INFO in ch.qos.logback.core.sift.SiftProcessor@282c5ce1 - End of configuration. [testng] [2024-04-23 06:59:48,568] [pool-1-thread-9] Initializing /data/nico/test-ASI-Z_181/img_000000004_Cy3_006.tif: [testng] 06:59:48,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 06:59:48,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:59:48,569 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-23_06-59-48.log] [testng] 06:59:48,570 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7de6c001 - End of configuration. [testng] [2024-04-23 06:59:48,784] [pool-1-thread-9] Used files list does not include base file [testng] [2024-04-23 06:59:48,787] [pool-1-thread-8] Initializing /data/public/1.4.16/serge/Pos4/img_000000000_00-BF0_000.tif: [testng] 06:59:48,787 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 06:59:48,787 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:59:48,788 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-23_06-59-48.log] [testng] 06:59:48,788 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26d5f342 - End of configuration. [testng] [2024-04-23 06:59:49,009] [pool-1-thread-7] Initializing /data/nico/test_1/Acqusition.xml: [testng] 06:59:49,010 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 06:59:49,010 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:59:49,011 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-23_06-59-49.log] [testng] 06:59:49,011 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f8f2e8d - End of configuration. [testng] [2024-04-23 06:59:49,072] [pool-1-thread-6] Initializing /data/public/1.4.22/thomas/test/test_sep/Pos0/img_000000000_FITC_000.tif: [testng] 06:59:49,073 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 06:59:49,073 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:59:49,073 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-23_06-59-49.log] [testng] 06:59:49,074 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26d19575 - End of configuration. [testng] [2024-04-23 06:59:49,104] [pool-1-thread-5] Initializing /data/public/1.4.23/jens/fucci_GFP-geminin_RFP-cdt1_2_MMStack_Pos0_metadata.txt: [testng] 06:59:49,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 06:59:49,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:59:49,105 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-23_06-59-49.log] [testng] 06:59:49,106 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c28c5dc - End of configuration. [testng] [2024-04-23 06:59:50,161] [pool-1-thread-4] Initializing /data/nico/test-ASI-Z_181/img_000000004_FITC_009.tif: [testng] 06:59:50,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 06:59:50,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:59:50,162 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-23_06-59-50.log] [testng] 06:59:50,163 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f3e043d - End of configuration. [testng] [2024-04-23 06:59:50,295] [pool-1-thread-4] Used files list does not include base file [testng] [2024-04-23 06:59:50,298] [pool-1-thread-3] Initializing /data/nico/test-ASI-Z_181/img_000000004_Cy3_009.tif: [testng] 06:59:50,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 06:59:50,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:59:50,299 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-23_06-59-50.log] [testng] 06:59:50,300 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75254351 - End of configuration. [testng] [2024-04-23 06:59:50,400] [pool-1-thread-3] Used files list does not include base file [testng] [2024-04-23 06:59:50,403] [pool-1-thread-2] Initializing /data/nico/Untitled_4_multi_file/img_000000000_gfpFast_000.tif: [testng] 06:59:50,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 06:59:50,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:59:50,404 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-23_06-59-50.log] [testng] 06:59:50,404 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5664cade - End of configuration. [testng] [2024-04-23 06:59:51,925] [pool-1-thread-1] Initializing /data/public/1.4.22/thomas/test/test2_sep/Pos0/metadata.txt: [testng] [2024-04-23 06:59:52,722] [pool-1-thread-6] Initializing /data/pr-3229/1.4-large-acq-take-2_1_MMStack_Pos0_metadata.txt: time="2024-04-23T06:00:26Z" level=error msg="error waiting for container: unexpected EOF" Build step 'Execute shell' marked build as failure Finished: FAILURE