Started by upstream project "BIOFORMATS-test-repo" build number 19 originally caused by: Started by upstream project "Trigger" build number 22 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/jenkins9161973786530610189.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_2328_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] 01:39:23,841 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:39:23,842 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 01:39:23,842 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:39:23,843 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:39:23,844 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:39:23,844 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:39:23,844 |-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] 01:39:23,844 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:39:23,844 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:39:23,845 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:39:23,845 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:39:23,845 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:39:24,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:39:24,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:39:24,095 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:39:24,095 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:39:24,103 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:39:24,103 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:39:24,103 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:39:24,104 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:39:24,104 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 01:39:24,105 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 01:39:24,105 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 261 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-01 01:39:24,114] [main] java.version = 1.8.0_342 [testng] 01:39:24,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:39:24,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:24,161 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-01_01-39-24.log] [testng] 01:39:24,163 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-04-01 01:39:24,165] [main] testng.directory = /data [testng] [2024-04-01 01:39:24,165] [main] testng.configDirectory = /config [testng] [2024-04-01 01:39:24,176] [main] testng.multiplier = 1.0 [testng] [2024-04-01 01:39:24,176] [main] testng.in-memory = false [testng] [2024-04-01 01:39:24,177] [main] testng.allow-missing = false [testng] [2024-04-01 01:39:24,177] [main] user.language = fr [testng] [2024-04-01 01:39:24,177] [main] user.country = FR [testng] [2024-04-01 01:39:24,177] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-04-01 01:39:25,355] [main] ---------------------------------------- [testng] [2024-04-01 01:39:25,355] [main] Total files: 20 [testng] [2024-04-01 01:39:25,355] [main] Scan time: 1.178 s (58 ms/file) [testng] [2024-04-01 01:39:25,356] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-01 01:39:25,905] [pool-1-thread-1] Initializing /data/ascb/c191.st: [testng] 01:39:25,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:39:25,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:25,906 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-01_01-39-25.log] [testng] 01:39:25,906 |-INFO in ch.qos.logback.core.sift.SiftProcessor@148bf50b - End of configuration. [testng] [2024-04-01 01:39:25,924] [pool-1-thread-12] Initializing /data/dan/one.mrc: [testng] 01:39:25,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:39:25,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:25,925 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-01_01-39-25.log] [testng] 01:39:25,925 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76a818e - End of configuration. [testng] [2024-04-01 01:39:25,936] [pool-1-thread-11] Initializing /data/bioformats2raw-198/test_uint8.mrc: [testng] 01:39:25,936 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:39:25,936 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:25,937 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-01_01-39-25.log] [testng] 01:39:25,937 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67cac8cd - End of configuration. [testng] [2024-04-01 01:39:25,944] [pool-1-thread-10] Initializing /data/ascb/c191ali.mrc: [testng] 01:39:25,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:39:25,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:25,944 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-01_01-39-25.log] [testng] 01:39:25,945 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f61e7d3 - End of configuration. [testng] [2024-04-01 01:39:25,956] [pool-1-thread-9] Initializing /data/strand/Series1_A.mrc: [testng] 01:39:25,956 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:39:25,956 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:25,956 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-01_01-39-25.log] [testng] 01:39:25,957 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7206136c - End of configuration. [testng] [2024-04-01 01:39:25,967] [pool-1-thread-8] Initializing /data/dan/two.mrc: [testng] 01:39:25,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:39:25,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:25,968 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-01_01-39-25.log] [testng] 01:39:25,969 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a0e939b - End of configuration. [testng] [2024-04-01 01:39:25,981] [pool-1-thread-7] Initializing /data/samples/golgi.mrc: [testng] 01:39:25,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:39:25,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:25,982 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-01_01-39-25.log] [testng] 01:39:25,982 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5efa6fcf - End of configuration. [testng] [2024-04-01 01:39:25,994] [pool-1-thread-6] Initializing /data/ticket-10073/wtjoin4.rec: [testng] 01:39:25,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:39:25,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:25,994 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-01_01-39-25.log] [testng] 01:39:25,995 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59149c41 - End of configuration. [testng] [2024-04-01 01:39:26,005] [pool-1-thread-5] Initializing /data/jcb/thyl-apr23-4.rec: [testng] 01:39:26,005 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:39:26,005 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:26,006 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-01_01-39-26.log] [testng] 01:39:26,006 |-INFO in ch.qos.logback.core.sift.SiftProcessor@425e85f3 - End of configuration. [testng] [2024-04-01 01:39:26,018] [pool-1-thread-4] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc: [testng] 01:39:26,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:39:26,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:26,019 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-01_01-39-26.log] [testng] 01:39:26,019 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a60b573 - End of configuration. [testng] [2024-04-01 01:39:26,068] [pool-1-thread-3] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: [testng] 01:39:26,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:39:26,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:26,069 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-01_01-39-26.log] [testng] 01:39:26,069 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bee1669 - End of configuration. [testng] [2024-04-01 01:39:26,102] [pool-1-thread-2] Initializing /data/ascb/514_9903.mrc: [testng] 01:39:26,102 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:39:26,102 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:39:26,103 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-01_01-39-26.log] [testng] 01:39:26,103 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a4a49ba - End of configuration. [testng] [2024-04-01 01:39:27,707] [pool-1-thread-11] Initializing /data/dan/three.mrc: [testng] [2024-04-01 01:39:27,716] [pool-1-thread-3] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: [testng] [2024-04-01 01:39:27,725] [pool-1-thread-7] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: [testng] [2024-04-01 01:39:27,734] [pool-1-thread-5] Initializing /data/jcb/thylakoid5.rec: [testng] [2024-04-01 01:39:27,741] [pool-1-thread-1] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc: [testng] [2024-04-01 01:39:27,748] [pool-1-thread-10] Initializing /data/ascb/cfa1071.mrc: [testng] [2024-04-01 01:39:28,285] [pool-1-thread-7] Initializing /data/samples/1160.mrc: [testng] [2024-04-01 01:39:28,907] [pool-1-thread-6] 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: 13 seconds Finished: SUCCESS