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Started by upstream project "BIOFORMATS-test-repo" build number 219 originally caused by: Started by upstream project "Trigger" build number 246 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins5988332850778512148.sh + '[' mrc = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_34756_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] 1 warning 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] 02:16:24,883 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:16:24,884 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 02:16:24,884 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:16:24,885 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:16:24,886 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:16:24,886 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:16:24,887 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:16:24,887 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:16:24,887 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:16:24,888 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:16:24,889 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:16:24,889 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:16:25,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:16:25,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:16:25,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:16:25,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:16:25,110 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:16:25,110 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:16:25,111 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:16:25,111 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:16:25,111 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 02:16:25,112 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 02:16:25,112 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 225 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-13 02:16:25,121] [main] java.version = 17.0.2 [testng] 02:16:25,124 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:16:25,124 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:25,183 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-13_02-16-25.log] [testng] 02:16:25,184 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-10-13 02:16:25,186] [main] testng.directory = /data [testng] [2024-10-13 02:16:25,187] [main] testng.configDirectory = /config [testng] [2024-10-13 02:16:25,195] [main] testng.multiplier = 1.0 [testng] [2024-10-13 02:16:25,196] [main] testng.in-memory = false [testng] [2024-10-13 02:16:25,196] [main] testng.allow-missing = false [testng] [2024-10-13 02:16:25,196] [main] user.language = en [testng] [2024-10-13 02:16:25,196] [main] user.country = ${user.country} [testng] [2024-10-13 02:16:25,196] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-13 02:16:37,420] [main] ---------------------------------------- [testng] [2024-10-13 02:16:37,420] [main] Total files: 20 [testng] [2024-10-13 02:16:37,420] [main] Scan time: 12.224 s (611 ms/file) [testng] [2024-10-13 02:16:37,420] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-13 02:16:49,425] [pool-1-thread-1] Initializing /data/dan/one.mrc: [testng] 02:16:49,425 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:16:49,425 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:49,426 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-13_02-16-49.log] [testng] 02:16:49,427 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c9a204b - End of configuration. [testng] [2024-10-13 02:16:49,889] [pool-1-thread-12] Initializing /data/samples/1160.mrc: [testng] 02:16:49,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:16:49,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:49,890 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-13_02-16-49.log] [testng] 02:16:49,890 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e31cb29 - End of configuration. [testng] [2024-10-13 02:16:50,415] [pool-1-thread-11] Initializing /data/ascb/c191ali.mrc: [testng] 02:16:50,416 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:16:50,416 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:50,417 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-13_02-16-50.log] [testng] 02:16:50,417 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a43bc67 - End of configuration. [testng] [2024-10-13 02:16:51,472] [pool-1-thread-10] Initializing /data/bioformats2raw-198/test_uint8.mrc: [testng] 02:16:51,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:16:51,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:51,473 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-13_02-16-51.log] [testng] 02:16:51,474 |-INFO in ch.qos.logback.core.sift.SiftProcessor@678253fa - End of configuration. [testng] [2024-10-13 02:16:52,201] [pool-1-thread-9] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: [testng] 02:16:52,201 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:16:52,201 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:52,202 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-13_02-16-52.log] [testng] 02:16:52,202 |-INFO in ch.qos.logback.core.sift.SiftProcessor@528b6fee - End of configuration. [testng] [2024-10-13 02:16:53,347] [pool-1-thread-8] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc: [testng] 02:16:53,348 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:16:53,348 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:53,348 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-13_02-16-53.log] [testng] 02:16:53,349 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e3710da - End of configuration. [testng] [2024-10-13 02:16:53,818] [pool-1-thread-7] Initializing /data/jcb/thylakoid5.rec: [testng] 02:16:53,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:16:53,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:53,819 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-13_02-16-53.log] [testng] 02:16:53,819 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e206dd - End of configuration. [testng] [2024-10-13 02:16:54,159] [pool-1-thread-6] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: [testng] 02:16:54,159 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:16:54,159 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:54,160 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-13_02-16-54.log] [testng] 02:16:54,160 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c0165b7 - End of configuration. [testng] [2024-10-13 02:16:54,612] [pool-1-thread-5] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: [testng] 02:16:54,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:16:54,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:54,613 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-13_02-16-54.log] [testng] 02:16:54,614 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a49712d - End of configuration. [testng] [2024-10-13 02:16:55,147] [pool-1-thread-4] Initializing /data/dan/three.mrc: [testng] 02:16:55,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:16:55,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:55,148 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-13_02-16-55.log] [testng] 02:16:55,148 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34aaa8c2 - End of configuration. [testng] [2024-10-13 02:16:55,713] [pool-1-thread-3] Initializing /data/ascb/cfa1071.mrc: [testng] 02:16:55,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:16:55,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:55,714 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-13_02-16-55.log] [testng] 02:16:55,715 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c1e8179 - End of configuration. [testng] [2024-10-13 02:16:56,125] [pool-1-thread-2] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: [testng] 02:16:56,125 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:16:56,125 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:56,126 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-13_02-16-56.log] [testng] 02:16:56,126 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5bc12d6 - End of configuration. [testng] [2024-10-13 02:17:02,166] [pool-1-thread-5] Initializing /data/ticket-10073/wtjoin4.rec: [testng] [2024-10-13 02:17:02,610] [pool-1-thread-9] Initializing /data/jcb/thyl-apr23-4.rec: [testng] [2024-10-13 02:17:03,004] [pool-1-thread-10] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc: [testng] [2024-10-13 02:17:03,465] [pool-1-thread-2] Initializing /data/samples/golgi.mrc: [testng] [2024-10-13 02:17:04,137] [pool-1-thread-6] Initializing /data/ascb/c191.st: [testng] [2024-10-13 02:17:04,550] [pool-1-thread-11] Initializing /data/dan/two.mrc: [testng] [2024-10-13 02:17:04,932] [pool-1-thread-7] Initializing /data/ascb/514_9903.mrc: [testng] [2024-10-13 02:17:05,434] [pool-1-thread-1] Initializing /data/strand/Series1_A.mrc: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1060, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 51 seconds Finished: SUCCESS