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Started by upstream project "BIOFORMATS-test-repo" build number 227 originally caused by: Started by upstream project "Trigger" build number 252 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins16746253257630065725.sh + '[' mrc = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35603_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 test-automated: [testng] File leak detector installed [testng] 10:18:11,958 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 10:18:11,960 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 10:18:11,960 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:18:11,961 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:18:11,961 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 10:18:11,962 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 10:18:11,962 |-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] 10:18:11,962 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:18:11,962 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:18:11,963 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 10:18:11,963 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 10:18:11,963 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 10:18:12,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 10:18:12,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 10:18:12,214 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 10:18:12,214 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 10:18:12,222 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 10:18:12,222 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 10:18:12,222 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 10:18:12,223 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 10:18:12,223 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 10:18:12,224 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 10:18:12,224 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 262 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-18 10:18:12,234] [main] java.version = 1.8.0_342 [testng] 10:18:12,237 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 10:18:12,237 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:12,282 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-18_10-18-12.log] [testng] 10:18:12,284 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-10-18 10:18:12,285] [main] testng.directory = /data [testng] [2024-10-18 10:18:12,286] [main] testng.configDirectory = /config [testng] [2024-10-18 10:18:12,298] [main] testng.multiplier = 1.0 [testng] [2024-10-18 10:18:12,298] [main] testng.in-memory = false [testng] [2024-10-18 10:18:12,299] [main] testng.allow-missing = false [testng] [2024-10-18 10:18:12,299] [main] user.language = en [testng] [2024-10-18 10:18:12,299] [main] user.country = ${user.country} [testng] [2024-10-18 10:18:12,299] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-18 10:18:16,951] [main] ---------------------------------------- [testng] [2024-10-18 10:18:16,952] [main] Total files: 20 [testng] [2024-10-18 10:18:16,952] [main] Scan time: 4.652 s (232 ms/file) [testng] [2024-10-18 10:18:16,952] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-18 10:18:22,796] [pool-1-thread-1] Initializing /data/ascb/514_9903.mrc: [testng] 10:18:22,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 10:18:22,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:22,797 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-18_10-18-22.log] [testng] 10:18:22,797 |-INFO in ch.qos.logback.core.sift.SiftProcessor@490bc666 - End of configuration. [testng] [2024-10-18 10:18:23,147] [pool-1-thread-12] Initializing /data/samples/golgi.mrc: [testng] 10:18:23,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 10:18:23,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:23,148 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-18_10-18-23.log] [testng] 10:18:23,148 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2887a585 - End of configuration. [testng] [2024-10-18 10:18:23,447] [pool-1-thread-11] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: [testng] 10:18:23,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 10:18:23,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:23,448 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-18_10-18-23.log] [testng] 10:18:23,448 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12d84b91 - End of configuration. [testng] [2024-10-18 10:18:23,715] [pool-1-thread-10] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: [testng] 10:18:23,716 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 10:18:23,716 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:23,717 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-18_10-18-23.log] [testng] 10:18:23,717 |-INFO in ch.qos.logback.core.sift.SiftProcessor@121a8527 - End of configuration. [testng] [2024-10-18 10:18:23,970] [pool-1-thread-9] Initializing /data/samples/1160.mrc: [testng] 10:18:23,970 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 10:18:23,970 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:23,971 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-18_10-18-23.log] [testng] 10:18:23,971 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28c5962e - End of configuration. [testng] [2024-10-18 10:18:24,288] [pool-1-thread-8] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: [testng] 10:18:24,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 10:18:24,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:24,288 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-18_10-18-24.log] [testng] 10:18:24,289 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18b03250 - End of configuration. [testng] [2024-10-18 10:18:24,576] [pool-1-thread-7] Initializing /data/bioformats2raw-198/test_uint8.mrc: [testng] 10:18:24,577 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 10:18:24,577 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:24,577 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-18_10-18-24.log] [testng] 10:18:24,578 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30ba3aad - End of configuration. [testng] [2024-10-18 10:18:24,804] [pool-1-thread-6] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: [testng] 10:18:24,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 10:18:24,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:24,805 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-18_10-18-24.log] [testng] 10:18:24,805 |-INFO in ch.qos.logback.core.sift.SiftProcessor@317e9782 - End of configuration. [testng] [2024-10-18 10:18:25,038] [pool-1-thread-5] Initializing /data/jcb/thyl-apr23-4.rec: [testng] 10:18:25,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 10:18:25,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:25,040 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-18_10-18-25.log] [testng] 10:18:25,040 |-INFO in ch.qos.logback.core.sift.SiftProcessor@450312c5 - End of configuration. [testng] [2024-10-18 10:18:25,288] [pool-1-thread-4] Initializing /data/ascb/cfa1071.mrc: [testng] 10:18:25,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 10:18:25,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:25,299 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-18_10-18-25.log] [testng] 10:18:25,299 |-INFO in ch.qos.logback.core.sift.SiftProcessor@eb3ba8 - End of configuration. [testng] [2024-10-18 10:18:25,755] [pool-1-thread-3] Initializing /data/dan/one.mrc: [testng] 10:18:25,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 10:18:25,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:25,756 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-18_10-18-25.log] [testng] 10:18:25,777 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36a5f084 - End of configuration. [testng] [2024-10-18 10:18:25,982] [pool-1-thread-2] Initializing /data/dan/two.mrc: [testng] 10:18:25,982 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 10:18:25,982 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:18:25,983 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-18_10-18-25.log] [testng] 10:18:25,983 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b25bc0f - End of configuration. [testng] [2024-10-18 10:18:33,198] [pool-1-thread-7] Initializing /data/dan/three.mrc: [testng] [2024-10-18 10:18:33,454] [pool-1-thread-10] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc: [testng] [2024-10-18 10:18:33,759] [pool-1-thread-12] Initializing /data/strand/Series1_A.mrc: [testng] [2024-10-18 10:18:34,142] [pool-1-thread-6] Initializing /data/ticket-10073/wtjoin4.rec: [testng] [2024-10-18 10:18:34,546] [pool-1-thread-11] Initializing /data/jcb/thylakoid5.rec: [testng] [2024-10-18 10:18:34,809] [pool-1-thread-5] Initializing /data/ascb/c191ali.mrc: [testng] [2024-10-18 10:18:35,876] [pool-1-thread-8] Initializing /data/ascb/c191.st: [testng] [2024-10-18 10:18:36,667] [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: 36 seconds Finished: SUCCESS