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Started by upstream project "BIOFORMATS-test-repo" build number 225 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/jenkins17308084474806386318.sh + '[' mrc = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35491_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 [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings test-automated: [testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 14:42:59,608 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 14:42:59,610 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 14:42:59,610 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 14:42:59,610 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 14:42:59,611 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 14:42:59,611 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 14:42:59,611 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 14:42:59,611 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 14:42:59,612 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 14:42:59,612 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 14:42:59,613 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 14:42:59,613 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 14:42:59,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 14:42:59,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 14:42:59,784 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 14:42:59,784 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 14:42:59,790 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 14:42:59,790 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 14:42:59,790 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 14:42:59,791 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 14:42:59,791 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 14:42:59,791 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 14:42:59,792 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 180 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-17 14:42:59,800] [main] java.version = 21 [testng] 14:42:59,803 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 14:42:59,803 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:42:59,842 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-17_14-42-59.log] [testng] 14:42:59,843 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-10-17 14:42:59,845] [main] testng.directory = /data [testng] [2024-10-17 14:42:59,845] [main] testng.configDirectory = /config [testng] [2024-10-17 14:42:59,853] [main] testng.multiplier = 1.0 [testng] [2024-10-17 14:42:59,853] [main] testng.in-memory = false [testng] [2024-10-17 14:42:59,853] [main] testng.allow-missing = false [testng] [2024-10-17 14:42:59,853] [main] user.language = en [testng] [2024-10-17 14:42:59,853] [main] user.country = ${user.country} [testng] [2024-10-17 14:42:59,853] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-17 14:43:22,717] [main] ---------------------------------------- [testng] [2024-10-17 14:43:22,717] [main] Total files: 20 [testng] [2024-10-17 14:43:22,717] [main] Scan time: 22.863 s (1143 ms/file) [testng] [2024-10-17 14:43:22,717] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-17 14:43:54,652] [pool-1-thread-1] Initializing /data/jcb/thylakoid5.rec: [testng] 14:43:54,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 14:43:54,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:43:54,654 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-17_14-43-54.log] [testng] 14:43:54,654 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d7754be - End of configuration. [testng] [2024-10-17 14:43:56,595] [pool-1-thread-12] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc: [testng] 14:43:56,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 14:43:56,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:43:56,597 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-17_14-43-56.log] [testng] 14:43:56,598 |-INFO in ch.qos.logback.core.sift.SiftProcessor@109be9ad - End of configuration. [testng] [2024-10-17 14:43:58,866] [pool-1-thread-11] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: [testng] 14:43:58,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 14:43:58,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:43:58,867 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-17_14-43-58.log] [testng] 14:43:58,868 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2afd0497 - End of configuration. [testng] [2024-10-17 14:44:01,019] [pool-1-thread-10] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc: [testng] 14:44:01,019 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 14:44:01,019 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:44:01,020 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-17_14-44-01.log] [testng] 14:44:01,021 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e4110fc - End of configuration. [testng] [2024-10-17 14:44:03,299] [pool-1-thread-9] Initializing /data/strand/Series1_A.mrc: [testng] 14:44:03,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 14:44:03,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:44:03,300 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-17_14-44-03.log] [testng] 14:44:03,300 |-INFO in ch.qos.logback.core.sift.SiftProcessor@644f4ccc - End of configuration. [testng] [2024-10-17 14:44:04,979] [pool-1-thread-8] Initializing /data/ascb/c191ali.mrc: [testng] 14:44:04,979 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 14:44:04,979 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:44:04,980 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-17_14-44-04.log] [testng] 14:44:04,980 |-INFO in ch.qos.logback.core.sift.SiftProcessor@788b2ea1 - End of configuration. [testng] [2024-10-17 14:44:06,810] [pool-1-thread-7] Initializing /data/ascb/cfa1071.mrc: [testng] 14:44:06,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 14:44:06,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:44:06,811 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-17_14-44-06.log] [testng] 14:44:06,812 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e92f434 - End of configuration. [testng] [2024-10-17 14:44:08,602] [pool-1-thread-6] Initializing /data/samples/1160.mrc: [testng] 14:44:08,602 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 14:44:08,602 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:44:08,603 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-17_14-44-08.log] [testng] 14:44:08,604 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b60ca87 - End of configuration. [testng] [2024-10-17 14:44:09,730] [pool-1-thread-5] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: [testng] 14:44:09,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 14:44:09,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:44:09,731 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-17_14-44-09.log] [testng] 14:44:09,732 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3948f91c - End of configuration. [testng] [2024-10-17 14:44:11,595] [pool-1-thread-4] Initializing /data/dan/one.mrc: [testng] 14:44:11,595 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 14:44:11,595 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:44:11,596 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-17_14-44-11.log] [testng] 14:44:11,596 |-INFO in ch.qos.logback.core.sift.SiftProcessor@629bcc5b - End of configuration. [testng] [2024-10-17 14:44:14,067] [pool-1-thread-3] Initializing /data/samples/golgi.mrc: [testng] 14:44:14,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 14:44:14,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:44:14,068 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-17_14-44-14.log] [testng] 14:44:14,068 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43cde3e7 - End of configuration. [testng] [2024-10-17 14:44:15,854] [pool-1-thread-2] Initializing /data/dan/two.mrc: [testng] 14:44:15,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 14:44:15,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:44:15,855 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-17_14-44-15.log] [testng] 14:44:15,855 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a18c3dd - End of configuration. [testng] [2024-10-17 14:44:34,482] [pool-1-thread-3] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: [testng] [2024-10-17 14:44:35,937] [pool-1-thread-1] Initializing /data/ascb/c191.st: [testng] [2024-10-17 14:44:37,398] [pool-1-thread-11] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: [testng] [2024-10-17 14:44:38,607] [pool-1-thread-5] Initializing /data/ticket-10073/wtjoin4.rec: [testng] [2024-10-17 14:44:40,195] [pool-1-thread-8] Initializing /data/bioformats2raw-198/test_uint8.mrc: [testng] [2024-10-17 14:44:41,851] [pool-1-thread-4] Initializing /data/dan/three.mrc: [testng] [2024-10-17 14:44:43,989] [pool-1-thread-10] Initializing /data/ascb/514_9903.mrc: [testng] [2024-10-17 14:44:45,965] [pool-1-thread-2] Initializing /data/jcb/thyl-apr23-4.rec: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1060, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 2 minutes 8 seconds Finished: SUCCESS