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Started by upstream project "BIOFORMATS-test-repo" build number 282 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins2604892498442570228.sh + '[' mrc = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_44497_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] 10:46:55,720 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 10:46:55,721 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 10:46:55,721 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:46:55,722 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:46:55,722 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 10:46:55,723 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 10:46:55,723 |-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] 10:46:55,723 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:46:55,723 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:46:55,724 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 10:46:55,724 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 10:46:55,724 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 10:46:55,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 10:46:55,960 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 10:46:55,988 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 10:46:55,988 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 10:46:55,996 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 10:46:55,997 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 10:46:55,997 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 10:46:55,997 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 10:46:55,997 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 10:46:55,998 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 10:46:55,998 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 275 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-06 10:46:56,008] [main] java.version = 1.8.0_342 [testng] 10:46:56,012 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 10:46:56,012 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:46:56,057 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-06_10-46-56.log] [testng] 10:46:56,059 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-06 10:46:56,061] [main] testng.directory = /data [testng] [2024-12-06 10:46:56,061] [main] testng.configDirectory = /config [testng] [2024-12-06 10:46:56,073] [main] testng.multiplier = 1.0 [testng] [2024-12-06 10:46:56,074] [main] testng.in-memory = false [testng] [2024-12-06 10:46:56,074] [main] testng.allow-missing = false [testng] [2024-12-06 10:46:56,074] [main] user.language = en [testng] [2024-12-06 10:46:56,074] [main] user.country = ${user.country} [testng] [2024-12-06 10:46:56,074] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-06 10:47:04,787] [main] ---------------------------------------- [testng] [2024-12-06 10:47:04,787] [main] Total files: 20 [testng] [2024-12-06 10:47:04,787] [main] Scan time: 8.713 s (435 ms/file) [testng] [2024-12-06 10:47:04,787] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-06 10:47:07,934] [pool-1-thread-1] Initializing /data/ascb/514_9903.mrc: [testng] 10:47:07,934 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 10:47:07,934 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:47:07,935 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-06_10-47-07.log] [testng] 10:47:07,936 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e7b9e09 - End of configuration. [testng] [2024-12-06 10:47:08,090] [pool-1-thread-12] Initializing /data/samples/golgi.mrc: [testng] 10:47:08,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 10:47:08,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:47:08,091 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-06_10-47-08.log] [testng] 10:47:08,091 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e98000b - End of configuration. [testng] [2024-12-06 10:47:08,265] [pool-1-thread-11] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: [testng] 10:47:08,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 10:47:08,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:47:08,266 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-06_10-47-08.log] [testng] 10:47:08,267 |-INFO in ch.qos.logback.core.sift.SiftProcessor@402f89ea - End of configuration. [testng] [2024-12-06 10:47:08,414] [pool-1-thread-10] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: [testng] 10:47:08,415 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 10:47:08,415 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:47:08,415 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-06_10-47-08.log] [testng] 10:47:08,416 |-INFO in ch.qos.logback.core.sift.SiftProcessor@453b05b6 - End of configuration. [testng] [2024-12-06 10:47:08,567] [pool-1-thread-9] Initializing /data/samples/1160.mrc: [testng] 10:47:08,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 10:47:08,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:47:08,568 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-06_10-47-08.log] [testng] 10:47:08,569 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56bc7b84 - End of configuration. [testng] [2024-12-06 10:47:08,718] [pool-1-thread-8] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: [testng] 10:47:08,718 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 10:47:08,718 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:47:08,719 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-06_10-47-08.log] [testng] 10:47:08,719 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7318d48f - End of configuration. [testng] [2024-12-06 10:47:08,864] [pool-1-thread-7] Initializing /data/bioformats2raw-198/test_uint8.mrc: [testng] 10:47:08,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 10:47:08,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:47:08,865 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-06_10-47-08.log] [testng] 10:47:08,866 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1118801a - End of configuration. [testng] [2024-12-06 10:47:09,038] [pool-1-thread-6] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: [testng] 10:47:09,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 10:47:09,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:47:09,039 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-06_10-47-09.log] [testng] 10:47:09,039 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71d3cffd - End of configuration. [testng] [2024-12-06 10:47:09,185] [pool-1-thread-5] Initializing /data/jcb/thyl-apr23-4.rec: [testng] 10:47:09,185 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 10:47:09,185 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:47:09,186 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-06_10-47-09.log] [testng] 10:47:09,186 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c958798 - End of configuration. [testng] [2024-12-06 10:47:09,331] [pool-1-thread-4] Initializing /data/ascb/cfa1071.mrc: [testng] 10:47:09,331 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 10:47:09,331 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:47:09,342 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-06_10-47-09.log] [testng] 10:47:09,342 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7adc9d12 - End of configuration. [testng] [2024-12-06 10:47:09,478] [pool-1-thread-3] Initializing /data/dan/one.mrc: [testng] 10:47:09,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 10:47:09,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:47:09,479 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-06_10-47-09.log] [testng] 10:47:09,499 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1dd73262 - End of configuration. [testng] [2024-12-06 10:47:09,662] [pool-1-thread-2] Initializing /data/dan/two.mrc: [testng] 10:47:09,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 10:47:09,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:47:09,663 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-06_10-47-09.log] [testng] 10:47:09,663 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50557eb8 - End of configuration. [testng] [2024-12-06 10:47:13,591] [pool-1-thread-6] Initializing /data/dan/three.mrc: [testng] [2024-12-06 10:47:13,762] [pool-1-thread-7] Initializing /data/strand/Series1_A.mrc: [testng] [2024-12-06 10:47:13,918] [pool-1-thread-11] Initializing /data/ticket-10073/wtjoin4.rec: [testng] [2024-12-06 10:47:14,113] [pool-1-thread-8] Initializing /data/jcb/thylakoid5.rec: [testng] [2024-12-06 10:47:14,340] [pool-1-thread-10] Initializing /data/ascb/c191ali.mrc: [testng] [2024-12-06 10:47:14,541] [pool-1-thread-12] Initializing /data/ascb/c191.st: [testng] [2024-12-06 10:47:14,661] [pool-1-thread-5] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc: [testng] [2024-12-06 10:47:15,337] [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: 29 seconds Finished: SUCCESS