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Started by upstream project "BIOFORMATS-test-repo" build number 208 originally caused by: Started by upstream project "Trigger" build number 234 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/jenkins4680277004248790540.sh + '[' mrc = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_33004_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 01:49:32,031 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:49:32,033 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 01:49:32,033 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:49:32,033 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:49:32,034 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:49:32,034 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:49:32,034 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:49:32,034 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:49:32,035 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:49:32,035 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:49:32,036 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:49:32,036 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:49:32,189 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:49:32,189 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:49:32,213 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:49:32,213 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:49:32,219 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:49:32,219 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:49:32,219 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:49:32,220 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:49:32,220 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 01:49:32,221 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 01:49:32,221 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 186 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-03 01:49:32,229] [main] java.version = 21 [testng] 01:49:32,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:49:32,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:32,273 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-03_01-49-32.log] [testng] 01:49:32,274 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-10-03 01:49:32,276] [main] testng.directory = /data [testng] [2024-10-03 01:49:32,276] [main] testng.configDirectory = /config [testng] [2024-10-03 01:49:32,284] [main] testng.multiplier = 1.0 [testng] [2024-10-03 01:49:32,285] [main] testng.in-memory = false [testng] [2024-10-03 01:49:32,285] [main] testng.allow-missing = false [testng] [2024-10-03 01:49:32,285] [main] user.language = en [testng] [2024-10-03 01:49:32,285] [main] user.country = ${user.country} [testng] [2024-10-03 01:49:32,285] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-03 01:49:35,204] [main] ---------------------------------------- [testng] [2024-10-03 01:49:35,204] [main] Total files: 20 [testng] [2024-10-03 01:49:35,204] [main] Scan time: 2.919 s (145 ms/file) [testng] [2024-10-03 01:49:35,205] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-03 01:49:37,199] [pool-1-thread-1] Initializing /data/bioformats2raw-198/test_uint8.mrc: [testng] 01:49:37,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:49:37,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:37,201 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-03_01-49-37.log] [testng] 01:49:37,201 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ffd54ee - End of configuration. [testng] [2024-10-03 01:49:37,291] [pool-1-thread-12] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc: [testng] 01:49:37,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:49:37,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:37,293 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-03_01-49-37.log] [testng] 01:49:37,293 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a3a18c5 - End of configuration. [testng] [2024-10-03 01:49:37,382] [pool-1-thread-11] Initializing /data/dan/three.mrc: [testng] 01:49:37,382 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:49:37,382 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:37,383 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-03_01-49-37.log] [testng] 01:49:37,384 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c590946 - End of configuration. [testng] [2024-10-03 01:49:37,486] [pool-1-thread-10] Initializing /data/samples/golgi.mrc: [testng] 01:49:37,486 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:49:37,486 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:37,487 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-03_01-49-37.log] [testng] 01:49:37,487 |-INFO in ch.qos.logback.core.sift.SiftProcessor@456fdaeb - End of configuration. [testng] [2024-10-03 01:49:37,583] [pool-1-thread-9] Initializing /data/jcb/thylakoid5.rec: [testng] 01:49:37,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:49:37,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:37,584 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-03_01-49-37.log] [testng] 01:49:37,585 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6be4386f - End of configuration. [testng] [2024-10-03 01:49:37,680] [pool-1-thread-8] Initializing /data/ticket-10073/wtjoin4.rec: [testng] 01:49:37,680 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:49:37,680 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:37,681 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-03_01-49-37.log] [testng] 01:49:37,681 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f464403 - End of configuration. [testng] [2024-10-03 01:49:37,852] [pool-1-thread-7] Initializing /data/ascb/c191ali.mrc: [testng] 01:49:37,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:49:37,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:37,853 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-03_01-49-37.log] [testng] 01:49:37,853 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f395f6 - End of configuration. [testng] [2024-10-03 01:49:38,247] [pool-1-thread-6] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc: [testng] 01:49:38,247 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:49:38,247 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:38,248 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-03_01-49-38.log] [testng] 01:49:38,248 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b7e14b1 - End of configuration. [testng] [2024-10-03 01:49:38,353] [pool-1-thread-5] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: [testng] 01:49:38,354 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:49:38,354 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:38,355 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-03_01-49-38.log] [testng] 01:49:38,355 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a5ee39c - End of configuration. [testng] [2024-10-03 01:49:38,506] [pool-1-thread-4] Initializing /data/ascb/cfa1071.mrc: [testng] 01:49:38,507 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:49:38,507 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:38,508 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-03_01-49-38.log] [testng] 01:49:38,508 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dabef9a - End of configuration. [testng] [2024-10-03 01:49:38,689] [pool-1-thread-3] Initializing /data/strand/Series1_A.mrc: [testng] 01:49:38,689 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:49:38,690 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:38,690 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-03_01-49-38.log] [testng] 01:49:38,691 |-INFO in ch.qos.logback.core.sift.SiftProcessor@141e7d0c - End of configuration. [testng] [2024-10-03 01:49:38,798] [pool-1-thread-2] Initializing /data/samples/1160.mrc: [testng] 01:49:38,798 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:49:38,798 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:38,799 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-03_01-49-38.log] [testng] 01:49:38,799 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c8ecd7a - End of configuration. [testng] [2024-10-03 01:49:41,561] [pool-1-thread-1] Initializing /data/ascb/c191.st: [testng] [2024-10-03 01:49:41,643] [pool-1-thread-5] Initializing /data/ascb/514_9903.mrc: [testng] [2024-10-03 01:49:41,735] [pool-1-thread-10] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: [testng] [2024-10-03 01:49:41,845] [pool-1-thread-7] Initializing /data/dan/one.mrc: [testng] [2024-10-03 01:49:42,166] [pool-1-thread-6] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: [testng] [2024-10-03 01:49:42,405] [pool-1-thread-9] Initializing /data/jcb/thyl-apr23-4.rec: [testng] [2024-10-03 01:49:42,573] [pool-1-thread-11] Initializing /data/dan/two.mrc: [testng] [2024-10-03 01:49:42,738] [pool-1-thread-8] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1060, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 17 seconds Finished: SUCCESS