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Started by upstream project "BIOFORMATS-test-repo" build number 259 originally caused by: Started by upstream project "Trigger" build number 283 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins3304994839175362835.sh + '[' mrc = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_40852_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 -Duser.language=fr -Duser.country=FR 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 test-automated: [testng] File leak detector installed [testng] 00:52:42,688 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:52:42,690 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:52:42,690 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:52:42,691 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:52:42,691 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:52:42,691 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:52:42,692 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:52:42,692 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:52:42,692 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:52:42,692 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:52:42,693 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:52:42,693 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:52:42,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:52:42,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:52:42,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:52:42,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:52:42,948 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:52:42,949 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:52:42,949 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:52:42,949 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:52:42,949 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:52:42,950 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:52:42,950 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 258 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-18 00:52:42,965] [main] java.version = 1.8.0_342 [testng] 00:52:42,970 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:52:42,970 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:43,014 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-18_00-52-42.log] [testng] 00:52:43,016 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-18 00:52:43,018] [main] testng.directory = /data [testng] [2024-11-18 00:52:43,018] [main] testng.configDirectory = /config [testng] [2024-11-18 00:52:43,030] [main] testng.multiplier = 1.0 [testng] [2024-11-18 00:52:43,031] [main] testng.in-memory = false [testng] [2024-11-18 00:52:43,031] [main] testng.allow-missing = false [testng] [2024-11-18 00:52:43,031] [main] user.language = fr [testng] [2024-11-18 00:52:43,031] [main] user.country = FR [testng] [2024-11-18 00:52:43,031] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-18 00:52:48,137] [main] ---------------------------------------- [testng] [2024-11-18 00:52:48,137] [main] Total files: 20 [testng] [2024-11-18 00:52:48,137] [main] Scan time: 5.106 s (255 ms/file) [testng] [2024-11-18 00:52:48,137] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-18 00:52:52,908] [pool-1-thread-1] Initializing /data/ascb/514_9903.mrc: [testng] 00:52:52,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:52:52,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:52,909 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-18_00-52-52.log] [testng] 00:52:52,910 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3fd4c264 - End of configuration. [testng] [2024-11-18 00:52:53,141] [pool-1-thread-12] Initializing /data/samples/golgi.mrc: [testng] 00:52:53,141 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:52:53,141 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:53,142 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-18_00-52-53.log] [testng] 00:52:53,143 |-INFO in ch.qos.logback.core.sift.SiftProcessor@70b9facd - End of configuration. [testng] [2024-11-18 00:52:53,376] [pool-1-thread-11] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: [testng] 00:52:53,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:52:53,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:53,377 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-18_00-52-53.log] [testng] 00:52:53,377 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10114018 - End of configuration. [testng] [2024-11-18 00:52:53,578] [pool-1-thread-10] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: [testng] 00:52:53,578 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:52:53,578 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:53,579 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-18_00-52-53.log] [testng] 00:52:53,579 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18b03250 - End of configuration. [testng] [2024-11-18 00:52:53,797] [pool-1-thread-9] Initializing /data/samples/1160.mrc: [testng] 00:52:53,797 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:52:53,797 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:53,798 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-18_00-52-53.log] [testng] 00:52:53,798 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e5fcd4d - End of configuration. [testng] [2024-11-18 00:52:54,008] [pool-1-thread-8] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: [testng] 00:52:54,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:52:54,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:54,009 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-18_00-52-54.log] [testng] 00:52:54,009 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50557eb8 - End of configuration. [testng] [2024-11-18 00:52:54,236] [pool-1-thread-7] Initializing /data/bioformats2raw-198/test_uint8.mrc: [testng] 00:52:54,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:52:54,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:54,237 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-18_00-52-54.log] [testng] 00:52:54,237 |-INFO in ch.qos.logback.core.sift.SiftProcessor@105b377b - End of configuration. [testng] [2024-11-18 00:52:54,483] [pool-1-thread-6] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: [testng] 00:52:54,484 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:52:54,484 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:54,484 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-18_00-52-54.log] [testng] 00:52:54,485 |-INFO in ch.qos.logback.core.sift.SiftProcessor@eb3ba8 - End of configuration. [testng] [2024-11-18 00:52:54,678] [pool-1-thread-5] Initializing /data/jcb/thyl-apr23-4.rec: [testng] 00:52:54,678 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:52:54,678 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:54,679 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-18_00-52-54.log] [testng] 00:52:54,680 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dbbdc7f - End of configuration. [testng] [2024-11-18 00:52:54,878] [pool-1-thread-4] Initializing /data/ascb/cfa1071.mrc: [testng] 00:52:54,878 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:52:54,878 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:54,879 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-18_00-52-54.log] [testng] 00:52:54,889 |-INFO in ch.qos.logback.core.sift.SiftProcessor@424e8bb1 - End of configuration. [testng] [2024-11-18 00:52:55,119] [pool-1-thread-3] Initializing /data/dan/one.mrc: [testng] 00:52:55,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:52:55,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:55,120 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-18_00-52-55.log] [testng] 00:52:55,138 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36a5f084 - End of configuration. [testng] [2024-11-18 00:52:55,371] [pool-1-thread-2] Initializing /data/dan/two.mrc: [testng] 00:52:55,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:52:55,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:55,372 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-18_00-52-55.log] [testng] 00:52:55,373 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b25bc0f - End of configuration. [testng] [2024-11-18 00:52:59,628] [pool-1-thread-7] Initializing /data/dan/three.mrc: [testng] [2024-11-18 00:52:59,861] [pool-1-thread-6] Initializing /data/strand/Series1_A.mrc: [testng] [2024-11-18 00:53:00,068] [pool-1-thread-11] Initializing /data/ticket-10073/wtjoin4.rec: [testng] [2024-11-18 00:53:00,336] [pool-1-thread-12] Initializing /data/jcb/thylakoid5.rec: [testng] [2024-11-18 00:53:00,609] [pool-1-thread-5] Initializing /data/ascb/c191ali.mrc: [testng] [2024-11-18 00:53:00,982] [pool-1-thread-10] Initializing /data/ascb/c191.st: [testng] [2024-11-18 00:53:01,169] [pool-1-thread-8] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc: [testng] [2024-11-18 00:53:01,888] [pool-1-thread-3] 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: 28 seconds Finished: SUCCESS