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Started by upstream project "BIOFORMATS-test-repo" build number 231 originally caused by: Started by upstream project "Trigger" build number 256 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins10685066999185855876.sh + '[' mrc = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_36259_merge_ci -v /uod/idr/repos/curated/mrc:/data -v /uod/idr-scratch/merge-ci/curated/mrc:/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] 02:09:29,477 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:09:29,479 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 02:09:29,479 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:09:29,481 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:09:29,482 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:09:29,482 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:09:29,482 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:09:29,482 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:09:29,483 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:09:29,484 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:09:29,484 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:09:29,485 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:09:29,721 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:09:29,721 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:09:29,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:09:29,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:09:29,751 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:09:29,751 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:09:29,751 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:09:29,752 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:09:29,752 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 02:09:29,752 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 02:09:29,753 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 270 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-22 02:09:29,762] [main] java.version = 11.0.16 [testng] 02:09:29,765 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:09:29,765 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:29,808 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-22_02-09-29.log] [testng] 02:09:29,810 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-22 02:09:29,812] [main] testng.directory = /data [testng] [2024-10-22 02:09:29,812] [main] testng.configDirectory = /config [testng] [2024-10-22 02:09:29,822] [main] testng.multiplier = 1.0 [testng] [2024-10-22 02:09:29,823] [main] testng.in-memory = false [testng] [2024-10-22 02:09:29,823] [main] testng.allow-missing = false [testng] [2024-10-22 02:09:29,824] [main] user.language = en [testng] [2024-10-22 02:09:29,824] [main] user.country = ${user.country} [testng] [2024-10-22 02:09:29,824] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-22 02:09:40,431] [main] ---------------------------------------- [testng] [2024-10-22 02:09:40,431] [main] Total files: 20 [testng] [2024-10-22 02:09:40,431] [main] Scan time: 10.607 s (530 ms/file) [testng] [2024-10-22 02:09:40,431] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-22 02:09:53,964] [pool-1-thread-1] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc: [testng] 02:09:53,966 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:09:53,967 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:53,969 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-22_02-09-53.log] [testng] 02:09:53,970 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f5a9d4f - End of configuration. [testng] [2024-10-22 02:09:54,215] [pool-1-thread-12] Initializing /data/strand/Series1_A.mrc: [testng] 02:09:54,216 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:09:54,216 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:54,337 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-22_02-09-54.log] [testng] 02:09:54,338 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64ed2914 - End of configuration. [testng] [2024-10-22 02:09:54,589] [pool-1-thread-11] Initializing /data/ascb/c191.st: [testng] 02:09:54,590 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:09:54,590 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:54,590 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-22_02-09-54.log] [testng] 02:09:54,591 |-INFO in ch.qos.logback.core.sift.SiftProcessor@753f39c1 - End of configuration. [testng] [2024-10-22 02:09:55,481] [pool-1-thread-10] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: [testng] 02:09:55,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:09:55,482 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:55,482 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-22_02-09-55.log] [testng] 02:09:55,483 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4eaef7c8 - End of configuration. [testng] [2024-10-22 02:09:56,206] [pool-1-thread-9] Initializing /data/dan/two.mrc: [testng] 02:09:56,206 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:09:56,206 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:56,207 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-22_02-09-56.log] [testng] 02:09:56,207 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a3bbdd5 - End of configuration. [testng] [2024-10-22 02:09:57,046] [pool-1-thread-8] Initializing /data/ascb/cfa1071.mrc: [testng] 02:09:57,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:09:57,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:57,047 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-22_02-09-57.log] [testng] 02:09:57,047 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ec4cef8 - End of configuration. [testng] [2024-10-22 02:09:57,933] [pool-1-thread-7] Initializing /data/ascb/c191ali.mrc: [testng] 02:09:57,933 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:09:57,933 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:57,934 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-22_02-09-57.log] [testng] 02:09:57,934 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6de033c5 - End of configuration. [testng] [2024-10-22 02:09:58,187] [pool-1-thread-6] Initializing /data/jcb/thyl-apr23-4.rec: [testng] 02:09:58,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:09:58,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:58,188 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-22_02-09-58.log] [testng] 02:09:58,188 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14d9a16d - End of configuration. [testng] [2024-10-22 02:09:58,498] [pool-1-thread-5] Initializing /data/samples/1160.mrc: [testng] 02:09:58,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:09:58,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:58,499 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-22_02-09-58.log] [testng] 02:09:58,499 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67d52c4b - End of configuration. [testng] [2024-10-22 02:09:58,723] [pool-1-thread-4] Initializing /data/samples/golgi.mrc: [testng] 02:09:58,724 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:09:58,724 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:58,724 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-22_02-09-58.log] [testng] 02:09:58,725 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f6a066a - End of configuration. [testng] [2024-10-22 02:09:59,530] [pool-1-thread-3] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: [testng] 02:09:59,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:09:59,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:59,531 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-22_02-09-59.log] [testng] 02:09:59,531 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5544db0d - End of configuration. [testng] [2024-10-22 02:09:59,759] [pool-1-thread-2] Initializing /data/jcb/thylakoid5.rec: [testng] 02:09:59,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:09:59,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:59,760 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-22_02-09-59.log] [testng] 02:09:59,760 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b0af725 - End of configuration. [testng] [2024-10-22 02:10:06,146] [pool-1-thread-10] Initializing /data/bioformats2raw-198/test_uint8.mrc: [testng] [2024-10-22 02:10:06,369] [pool-1-thread-3] Initializing /data/ascb/514_9903.mrc: [testng] [2024-10-22 02:10:06,567] [pool-1-thread-6] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: [testng] [2024-10-22 02:10:07,150] [pool-1-thread-7] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: [testng] [2024-10-22 02:10:07,625] [pool-1-thread-4] Initializing /data/dan/three.mrc: [testng] [2024-10-22 02:10:08,520] [pool-1-thread-11] Initializing /data/dan/one.mrc: [testng] [2024-10-22 02:10:09,472] [pool-1-thread-2] Initializing /data/ticket-10073/wtjoin4.rec: [testng] [2024-10-22 02:10:11,135] [pool-1-thread-1] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1060, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 55 seconds Finished: SUCCESS