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Started by upstream project "BIOFORMATS-test-repo" build number 37 originally caused by: Started by upstream project "Trigger" build number 42 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins17382474354706597460.sh + '[' mrc = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_5116_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 01:34:07,867 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:34:07,868 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 01:34:07,868 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:34:07,869 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:34:07,870 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:34:07,870 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:34:07,870 |-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] 01:34:07,870 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:34:07,871 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:34:07,872 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:34:07,872 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:34:07,872 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:34:08,043 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:34:08,043 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:34:08,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:34:08,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:34:08,074 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:34:08,074 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:34:08,074 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:34:08,075 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:34:08,075 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 01:34:08,076 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 01:34:08,076 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 205 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-18 01:34:08,084] [main] java.version = 21 [testng] 01:34:08,088 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:34:08,088 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:08,128 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-18_01-34-08.log] [testng] 01:34:08,130 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-04-18 01:34:08,131] [main] testng.directory = /data [testng] [2024-04-18 01:34:08,131] [main] testng.configDirectory = /config [testng] [2024-04-18 01:34:08,140] [main] testng.multiplier = 1.0 [testng] [2024-04-18 01:34:08,141] [main] testng.in-memory = false [testng] [2024-04-18 01:34:08,141] [main] testng.allow-missing = false [testng] [2024-04-18 01:34:08,141] [main] user.language = en [testng] [2024-04-18 01:34:08,141] [main] user.country = ${user.country} [testng] [2024-04-18 01:34:08,141] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-04-18 01:34:09,504] [main] ---------------------------------------- [testng] [2024-04-18 01:34:09,504] [main] Total files: 20 [testng] [2024-04-18 01:34:09,504] [main] Scan time: 1.363 s (68 ms/file) [testng] [2024-04-18 01:34:09,505] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-18 01:34:09,954] [pool-1-thread-1] Initializing /data/samples/1160.mrc: [testng] 01:34:09,954 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:34:09,954 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:09,955 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-18_01-34-09.log] [testng] 01:34:09,956 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2feac026 - End of configuration. [testng] [2024-04-18 01:34:09,972] [pool-1-thread-12] Initializing /data/samples/golgi.mrc: [testng] 01:34:09,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:34:09,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:09,974 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-18_01-34-09.log] [testng] 01:34:09,975 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4088058 - End of configuration. [testng] [2024-04-18 01:34:09,985] [pool-1-thread-11] Initializing /data/ascb/514_9903.mrc: [testng] 01:34:09,986 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:34:09,986 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:09,986 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-18_01-34-09.log] [testng] 01:34:09,987 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53cfd0fa - End of configuration. [testng] [2024-04-18 01:34:10,038] [pool-1-thread-10] Initializing /data/ascb/cfa1071.mrc: [testng] 01:34:10,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:34:10,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:10,042 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-18_01-34-10.log] [testng] 01:34:10,042 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1627a0fd - End of configuration. [testng] [2024-04-18 01:34:10,156] [pool-1-thread-9] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc: [testng] 01:34:10,157 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:34:10,157 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:10,157 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-18_01-34-10.log] [testng] 01:34:10,158 |-INFO in ch.qos.logback.core.sift.SiftProcessor@226c77dd - End of configuration. [testng] [2024-04-18 01:34:10,173] [pool-1-thread-8] Initializing /data/jcb/thylakoid5.rec: [testng] 01:34:10,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:34:10,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:10,174 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-18_01-34-10.log] [testng] 01:34:10,174 |-INFO in ch.qos.logback.core.sift.SiftProcessor@142833ef - End of configuration. [testng] [2024-04-18 01:34:10,187] [pool-1-thread-7] Initializing /data/dan/two.mrc: [testng] 01:34:10,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:34:10,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:10,188 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-18_01-34-10.log] [testng] 01:34:10,188 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51d0f528 - End of configuration. [testng] [2024-04-18 01:34:10,204] [pool-1-thread-6] Initializing /data/bioformats2raw-198/test_uint8.mrc: [testng] 01:34:10,204 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:34:10,204 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:10,205 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-18_01-34-10.log] [testng] 01:34:10,206 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6de30792 - End of configuration. [testng] [2024-04-18 01:34:10,212] [pool-1-thread-5] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: [testng] 01:34:10,212 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:34:10,212 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:10,213 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-18_01-34-10.log] [testng] 01:34:10,214 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37c7e6ef - End of configuration. [testng] [2024-04-18 01:34:10,225] [pool-1-thread-4] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: [testng] 01:34:10,225 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:34:10,225 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:10,226 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-18_01-34-10.log] [testng] 01:34:10,227 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2af77d17 - End of configuration. [testng] [2024-04-18 01:34:10,238] [pool-1-thread-3] Initializing /data/dan/three.mrc: [testng] 01:34:10,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:34:10,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:10,239 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-18_01-34-10.log] [testng] 01:34:10,239 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65f17f60 - End of configuration. [testng] [2024-04-18 01:34:10,251] [pool-1-thread-2] Initializing /data/ascb/c191ali.mrc: [testng] 01:34:10,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:34:10,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:10,252 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-18_01-34-10.log] [testng] 01:34:10,252 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a89bd66 - End of configuration. [testng] [2024-04-18 01:34:11,731] [pool-1-thread-4] Initializing /data/ticket-10073/wtjoin4.rec: [testng] [2024-04-18 01:34:11,743] [pool-1-thread-6] Initializing /data/dan/one.mrc: [testng] [2024-04-18 01:34:11,755] [pool-1-thread-5] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc: [testng] [2024-04-18 01:34:11,767] [pool-1-thread-2] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: [testng] [2024-04-18 01:34:11,777] [pool-1-thread-12] Initializing /data/jcb/thyl-apr23-4.rec: [testng] [2024-04-18 01:34:11,834] [pool-1-thread-8] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: [testng] [2024-04-18 01:34:12,161] [pool-1-thread-12] Initializing /data/ascb/c191.st: [testng] [2024-04-18 01:34:12,173] [pool-1-thread-2] 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: 10 seconds Finished: SUCCESS