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Started by upstream project "BIOFORMATS-test-repo" build number 17 originally caused by: Started by upstream project "Trigger" build number 20 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/jenkins8424783865187590713.sh + '[' mrc = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_2000_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] 00:34:02,457 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:34:02,459 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 00:34:02,459 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:34:02,460 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:34:02,460 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:34:02,461 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:34:02,461 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:34:02,461 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:34:02,461 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:34:02,462 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:34:02,462 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:34:02,463 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:34:02,633 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:34:02,633 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:34:02,655 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:34:02,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:34:02,661 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:34:02,661 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:34:02,661 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:34:02,662 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:34:02,662 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 00:34:02,663 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 00:34:02,663 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 202 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-30 00:34:02,672] [main] java.version = 11.0.16 [testng] 00:34:02,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:34:02,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:02,717 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-30_00-34-02.log] [testng] 00:34:02,719 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-03-30 00:34:02,721] [main] testng.directory = /data [testng] [2024-03-30 00:34:02,721] [main] testng.configDirectory = /config [testng] [2024-03-30 00:34:02,731] [main] testng.multiplier = 1.0 [testng] [2024-03-30 00:34:02,732] [main] testng.in-memory = false [testng] [2024-03-30 00:34:02,732] [main] testng.allow-missing = false [testng] [2024-03-30 00:34:02,732] [main] user.language = en [testng] [2024-03-30 00:34:02,733] [main] user.country = ${user.country} [testng] [2024-03-30 00:34:02,733] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-30 00:34:04,191] [main] ---------------------------------------- [testng] [2024-03-30 00:34:04,192] [main] Total files: 20 [testng] [2024-03-30 00:34:04,192] [main] Scan time: 1.458 s (72 ms/file) [testng] [2024-03-30 00:34:04,192] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-30 00:34:04,749] [pool-1-thread-1] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: [testng] 00:34:04,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:34:04,751 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:04,753 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-30_00-34-04.log] [testng] 00:34:04,753 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24a41291 - End of configuration. [testng] [2024-03-30 00:34:04,775] [pool-1-thread-12] Initializing /data/ascb/c191.st: [testng] 00:34:04,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:34:04,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:04,777 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-30_00-34-04.log] [testng] 00:34:04,778 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bbc3868 - End of configuration. [testng] [2024-03-30 00:34:04,791] [pool-1-thread-11] Initializing /data/dan/two.mrc: [testng] 00:34:04,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:34:04,792 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:04,792 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-30_00-34-04.log] [testng] 00:34:04,793 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f464403 - End of configuration. [testng] [2024-03-30 00:34:04,810] [pool-1-thread-10] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc: [testng] 00:34:04,811 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:34:04,811 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:04,812 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-30_00-34-04.log] [testng] 00:34:04,812 |-INFO in ch.qos.logback.core.sift.SiftProcessor@342a5d84 - End of configuration. [testng] [2024-03-30 00:34:04,840] [pool-1-thread-9] Initializing /data/samples/golgi.mrc: [testng] 00:34:04,840 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:34:04,841 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:04,841 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-30_00-34-04.log] [testng] 00:34:04,842 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f395f6 - End of configuration. [testng] [2024-03-30 00:34:04,873] [pool-1-thread-8] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: [testng] 00:34:04,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:34:04,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:04,874 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-30_00-34-04.log] [testng] 00:34:04,874 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b7e14b1 - End of configuration. [testng] [2024-03-30 00:34:04,887] [pool-1-thread-7] Initializing /data/bioformats2raw-198/test_uint8.mrc: [testng] 00:34:04,888 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:34:04,888 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:04,888 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-30_00-34-04.log] [testng] 00:34:04,889 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a5ee39c - End of configuration. [testng] [2024-03-30 00:34:04,895] [pool-1-thread-6] Initializing /data/ascb/514_9903.mrc: [testng] 00:34:04,895 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:34:04,895 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:04,896 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-30_00-34-04.log] [testng] 00:34:04,896 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dabef9a - End of configuration. [testng] [2024-03-30 00:34:04,913] [pool-1-thread-5] Initializing /data/jcb/thyl-apr23-4.rec: [testng] 00:34:04,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:34:04,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:04,915 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-30_00-34-04.log] [testng] 00:34:04,915 |-INFO in ch.qos.logback.core.sift.SiftProcessor@141e7d0c - End of configuration. [testng] [2024-03-30 00:34:04,941] [pool-1-thread-4] Initializing /data/jcb/thylakoid5.rec: [testng] 00:34:04,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:34:04,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:04,942 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-30_00-34-04.log] [testng] 00:34:04,942 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c8ecd7a - End of configuration. [testng] [2024-03-30 00:34:04,956] [pool-1-thread-3] Initializing /data/dan/one.mrc: [testng] 00:34:04,957 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:34:04,957 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:04,957 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-30_00-34-04.log] [testng] 00:34:04,958 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5aeb3ed1 - End of configuration. [testng] [2024-03-30 00:34:04,969] [pool-1-thread-2] Initializing /data/ascb/cfa1071.mrc: [testng] 00:34:04,970 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:34:04,970 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:04,970 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-30_00-34-04.log] [testng] 00:34:04,971 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e1f4f9f - End of configuration. [testng] [2024-03-30 00:34:06,353] [pool-1-thread-7] Initializing /data/ascb/c191ali.mrc: [testng] [2024-03-30 00:34:06,363] [pool-1-thread-8] Initializing /data/ticket-10073/wtjoin4.rec: [testng] [2024-03-30 00:34:06,372] [pool-1-thread-9] Initializing /data/strand/Series1_A.mrc: [testng] [2024-03-30 00:34:06,382] [pool-1-thread-1] Initializing /data/samples/1160.mrc: [testng] [2024-03-30 00:34:06,560] [pool-1-thread-12] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: [testng] [2024-03-30 00:34:06,573] [pool-1-thread-5] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: [testng] [2024-03-30 00:34:06,584] [pool-1-thread-4] Initializing /data/dan/three.mrc: [testng] [2024-03-30 00:34:06,759] [pool-1-thread-3] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1060, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 12 seconds Finished: SUCCESS