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Started by upstream project "BIOFORMATS-test-repo" build number 237 originally caused by: Started by upstream project "Trigger" build number 262 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins13605105107859807316.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_37244_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] 01:10:13,754 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:10:13,756 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 01:10:13,756 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:10:13,757 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:10:13,757 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:10:13,757 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:10:13,758 |-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] 01:10:13,758 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:10:13,758 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:10:13,758 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:10:13,759 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:10:13,759 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:10:14,000 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:10:14,000 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:10:14,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:10:14,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:10:14,051 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:10:14,051 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:10:14,051 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:10:14,052 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:10:14,052 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 01:10:14,053 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 01:10:14,053 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 295 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-28 01:10:14,067] [main] java.version = 1.8.0_342 [testng] 01:10:14,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:10:14,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:10:14,132 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-28_01-10-14.log] [testng] 01:10:14,134 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-10-28 01:10:14,136] [main] testng.directory = /data [testng] [2024-10-28 01:10:14,136] [main] testng.configDirectory = /config [testng] [2024-10-28 01:10:14,149] [main] testng.multiplier = 1.0 [testng] [2024-10-28 01:10:14,149] [main] testng.in-memory = false [testng] [2024-10-28 01:10:14,149] [main] testng.allow-missing = false [testng] [2024-10-28 01:10:14,149] [main] user.language = fr [testng] [2024-10-28 01:10:14,149] [main] user.country = FR [testng] [2024-10-28 01:10:14,150] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-28 01:10:19,863] [main] ---------------------------------------- [testng] [2024-10-28 01:10:19,863] [main] Total files: 20 [testng] [2024-10-28 01:10:19,863] [main] Scan time: 5.713 s (285 ms/file) [testng] [2024-10-28 01:10:19,863] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-28 01:10:26,005] [pool-1-thread-1] Initializing /data/ascb/514_9903.mrc: [testng] 01:10:26,006 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:10:26,006 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:10:26,006 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-28_01-10-26.log] [testng] 01:10:26,007 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b7ff1b5 - End of configuration. [testng] [2024-10-28 01:10:26,354] [pool-1-thread-12] Initializing /data/samples/golgi.mrc: [testng] 01:10:26,355 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:10:26,355 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:10:26,356 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-28_01-10-26.log] [testng] 01:10:26,356 |-INFO in ch.qos.logback.core.sift.SiftProcessor@371a8719 - End of configuration. [testng] [2024-10-28 01:10:26,672] [pool-1-thread-11] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: [testng] 01:10:26,672 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:10:26,672 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:10:26,673 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-28_01-10-26.log] [testng] 01:10:26,674 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45e599aa - End of configuration. [testng] [2024-10-28 01:10:26,895] [pool-1-thread-10] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: [testng] 01:10:26,896 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:10:26,896 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:10:26,896 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-28_01-10-26.log] [testng] 01:10:26,897 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a812872 - End of configuration. [testng] [2024-10-28 01:10:27,095] [pool-1-thread-9] Initializing /data/samples/1160.mrc: [testng] 01:10:27,095 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:10:27,095 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:10:27,096 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-28_01-10-27.log] [testng] 01:10:27,096 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22903f9f - End of configuration. [testng] [2024-10-28 01:10:27,300] [pool-1-thread-8] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: [testng] 01:10:27,300 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:10:27,300 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:10:27,301 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-28_01-10-27.log] [testng] 01:10:27,301 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7edaa4bf - End of configuration. [testng] [2024-10-28 01:10:27,531] [pool-1-thread-7] Initializing /data/bioformats2raw-198/test_uint8.mrc: [testng] 01:10:27,531 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:10:27,531 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:10:27,532 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-28_01-10-27.log] [testng] 01:10:27,533 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57e88624 - End of configuration. [testng] [2024-10-28 01:10:27,778] [pool-1-thread-6] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: [testng] 01:10:27,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:10:27,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:10:27,779 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-28_01-10-27.log] [testng] 01:10:27,780 |-INFO in ch.qos.logback.core.sift.SiftProcessor@400f23bc - End of configuration. [testng] [2024-10-28 01:10:28,001] [pool-1-thread-5] Initializing /data/jcb/thyl-apr23-4.rec: [testng] 01:10:28,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:10:28,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:10:28,003 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-28_01-10-28.log] [testng] 01:10:28,003 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48841a3f - End of configuration. [testng] [2024-10-28 01:10:28,209] [pool-1-thread-4] Initializing /data/ascb/cfa1071.mrc: [testng] 01:10:28,209 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:10:28,209 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:10:28,229 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-28_01-10-28.log] [testng] 01:10:28,230 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58bb683f - End of configuration. [testng] [2024-10-28 01:10:28,432] [pool-1-thread-3] Initializing /data/dan/one.mrc: [testng] 01:10:28,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:10:28,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:10:28,433 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-28_01-10-28.log] [testng] 01:10:28,450 |-INFO in ch.qos.logback.core.sift.SiftProcessor@201d5a5b - End of configuration. [testng] [2024-10-28 01:10:28,681] [pool-1-thread-2] Initializing /data/dan/two.mrc: [testng] 01:10:28,682 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:10:28,682 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:10:28,682 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-28_01-10-28.log] [testng] 01:10:28,683 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74932b06 - End of configuration. [testng] [2024-10-28 01:10:33,658] [pool-1-thread-6] Initializing /data/dan/three.mrc: [testng] [2024-10-28 01:10:34,139] [pool-1-thread-7] Initializing /data/strand/Series1_A.mrc: [testng] [2024-10-28 01:10:34,533] [pool-1-thread-11] Initializing /data/ticket-10073/wtjoin4.rec: [testng] [2024-10-28 01:10:34,814] [pool-1-thread-12] Initializing /data/jcb/thylakoid5.rec: [testng] [2024-10-28 01:10:35,054] [pool-1-thread-10] Initializing /data/ascb/c191ali.mrc: [testng] [2024-10-28 01:10:35,321] [pool-1-thread-5] Initializing /data/ascb/c191.st: [testng] [2024-10-28 01:10:35,463] [pool-1-thread-8] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc: [testng] [2024-10-28 01:10:35,751] [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: 32 seconds Finished: SUCCESS