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Started by upstream project "BIOFORMATS-test-repo" build number 38 originally caused by: Started by upstream project "Trigger" build number 44 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/jenkins9994252429609629621.sh + '[' mrc = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_5280_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] 09:22:11,359 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 09:22:11,361 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 09:22:11,361 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:22:11,362 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:22:11,363 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 09:22:11,363 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 09:22:11,363 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 09:22:11,363 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:22:11,364 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:22:11,364 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 09:22:11,364 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 09:22:11,364 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 09:22:11,602 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 09:22:11,602 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 09:22:11,632 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 09:22:11,633 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 09:22:11,641 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 09:22:11,642 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 09:22:11,642 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 09:22:11,642 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 09:22:11,642 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 09:22:11,643 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 09:22:11,643 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 279 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-19 09:22:11,653] [main] java.version = 1.8.0_342 [testng] 09:22:11,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 09:22:11,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:22:11,708 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-19_09-22-11.log] [testng] 09:22:11,710 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-04-19 09:22:11,712] [main] testng.directory = /data [testng] [2024-04-19 09:22:11,712] [main] testng.configDirectory = /config [testng] [2024-04-19 09:22:11,727] [main] testng.multiplier = 1.0 [testng] [2024-04-19 09:22:11,727] [main] testng.in-memory = false [testng] [2024-04-19 09:22:11,727] [main] testng.allow-missing = false [testng] [2024-04-19 09:22:11,727] [main] user.language = en [testng] [2024-04-19 09:22:11,728] [main] user.country = ${user.country} [testng] [2024-04-19 09:22:11,728] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-04-19 09:22:12,921] [main] ---------------------------------------- [testng] [2024-04-19 09:22:12,921] [main] Total files: 20 [testng] [2024-04-19 09:22:12,921] [main] Scan time: 1.193 s (59 ms/file) [testng] [2024-04-19 09:22:12,921] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-19 09:22:13,551] [pool-1-thread-1] Initializing /data/ascb/c191.st: [testng] 09:22:13,551 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 09:22:13,552 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:22:13,552 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-19_09-22-13.log] [testng] 09:22:13,553 |-INFO in ch.qos.logback.core.sift.SiftProcessor@601c838d - End of configuration. [testng] [2024-04-19 09:22:13,572] [pool-1-thread-12] Initializing /data/dan/one.mrc: [testng] 09:22:13,572 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 09:22:13,572 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:22:13,573 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-19_09-22-13.log] [testng] 09:22:13,573 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47cb264 - End of configuration. [testng] [2024-04-19 09:22:13,584] [pool-1-thread-11] Initializing /data/bioformats2raw-198/test_uint8.mrc: [testng] 09:22:13,585 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 09:22:13,585 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:22:13,586 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-19_09-22-13.log] [testng] 09:22:13,586 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43c830b1 - End of configuration. [testng] [2024-04-19 09:22:13,593] [pool-1-thread-10] Initializing /data/ascb/c191ali.mrc: [testng] 09:22:13,593 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 09:22:13,593 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:22:13,594 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-19_09-22-13.log] [testng] 09:22:13,594 |-INFO in ch.qos.logback.core.sift.SiftProcessor@330e82a4 - End of configuration. [testng] [2024-04-19 09:22:13,605] [pool-1-thread-9] Initializing /data/strand/Series1_A.mrc: [testng] 09:22:13,605 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 09:22:13,605 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:22:13,606 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-19_09-22-13.log] [testng] 09:22:13,606 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78329d0a - End of configuration. [testng] [2024-04-19 09:22:13,619] [pool-1-thread-8] Initializing /data/dan/two.mrc: [testng] 09:22:13,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 09:22:13,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:22:13,620 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-19_09-22-13.log] [testng] 09:22:13,620 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5efa6fcf - End of configuration. [testng] [2024-04-19 09:22:13,632] [pool-1-thread-7] Initializing /data/samples/golgi.mrc: [testng] 09:22:13,633 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 09:22:13,633 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:22:13,633 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-19_09-22-13.log] [testng] 09:22:13,634 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3916efee - End of configuration. [testng] [2024-04-19 09:22:13,648] [pool-1-thread-6] Initializing /data/ticket-10073/wtjoin4.rec: [testng] 09:22:13,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 09:22:13,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:22:13,649 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-19_09-22-13.log] [testng] 09:22:13,649 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22578fc5 - End of configuration. [testng] [2024-04-19 09:22:13,661] [pool-1-thread-5] Initializing /data/jcb/thyl-apr23-4.rec: [testng] 09:22:13,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 09:22:13,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:22:13,662 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-19_09-22-13.log] [testng] 09:22:13,663 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68b0d3d5 - End of configuration. [testng] [2024-04-19 09:22:13,677] [pool-1-thread-4] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc: [testng] 09:22:13,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 09:22:13,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:22:13,678 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-19_09-22-13.log] [testng] 09:22:13,678 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a1349ad - End of configuration. [testng] [2024-04-19 09:22:13,721] [pool-1-thread-3] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: [testng] 09:22:13,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 09:22:13,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:22:13,722 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-19_09-22-13.log] [testng] 09:22:13,723 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c28c901 - End of configuration. [testng] [2024-04-19 09:22:13,753] [pool-1-thread-2] Initializing /data/ascb/514_9903.mrc: [testng] 09:22:13,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 09:22:13,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:22:13,754 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-19_09-22-13.log] [testng] 09:22:13,754 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e67bdd0 - End of configuration. [testng] [2024-04-19 09:22:15,293] [pool-1-thread-11] Initializing /data/dan/three.mrc: [testng] [2024-04-19 09:22:15,302] [pool-1-thread-3] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: [testng] [2024-04-19 09:22:15,314] [pool-1-thread-7] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: [testng] [2024-04-19 09:22:15,322] [pool-1-thread-5] Initializing /data/jcb/thylakoid5.rec: [testng] [2024-04-19 09:22:15,330] [pool-1-thread-10] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc: [testng] [2024-04-19 09:22:15,338] [pool-1-thread-1] Initializing /data/ascb/cfa1071.mrc: [testng] [2024-04-19 09:22:15,732] [pool-1-thread-7] Initializing /data/samples/1160.mrc: [testng] [2024-04-19 09:22:15,927] [pool-1-thread-12] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1060, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 14 seconds Finished: SUCCESS