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Started by upstream project "BIOFORMATS-test-repo" build number 306 originally caused by: Started by upstream project "Trigger" build number 328 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/jenkins8383951450250372947.sh + '[' mrc = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_48448_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 01:08:24,592 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:08:24,594 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 01:08:24,594 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:08:24,595 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:08:24,595 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:08:24,595 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:08:24,596 |-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] 01:08:24,596 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:08:24,596 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:08:24,597 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:08:24,597 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:08:24,597 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:08:24,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:08:24,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:08:24,780 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:08:24,780 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:08:24,786 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:08:24,786 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:08:24,786 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:08:24,787 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:08:24,787 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 01:08:24,788 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 01:08:24,788 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 192 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-02 01:08:24,797] [main] java.version = 21 [testng] 01:08:24,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:08:24,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:08:24,842 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-02_01-08-24.log] [testng] 01:08:24,844 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2025-01-02 01:08:24,845] [main] testng.directory = /data [testng] [2025-01-02 01:08:24,845] [main] testng.configDirectory = /config [testng] [2025-01-02 01:08:24,854] [main] testng.multiplier = 1.0 [testng] [2025-01-02 01:08:24,855] [main] testng.in-memory = false [testng] [2025-01-02 01:08:24,855] [main] testng.allow-missing = false [testng] [2025-01-02 01:08:24,855] [main] user.language = en [testng] [2025-01-02 01:08:24,855] [main] user.country = ${user.country} [testng] [2025-01-02 01:08:24,855] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-01-02 01:08:29,325] [main] ---------------------------------------- [testng] [2025-01-02 01:08:29,325] [main] Total files: 20 [testng] [2025-01-02 01:08:29,325] [main] Scan time: 4.47 s (223 ms/file) [testng] [2025-01-02 01:08:29,325] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-02 01:08:33,375] [pool-1-thread-1] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: [testng] 01:08:33,375 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:08:33,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:08:33,377 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-02_01-08-33.log] [testng] 01:08:33,377 |-INFO in ch.qos.logback.core.sift.SiftProcessor@412cf9f4 - End of configuration. [testng] [2025-01-02 01:08:33,542] [pool-1-thread-12] Initializing /data/dan/one.mrc: [testng] 01:08:33,542 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:08:33,542 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:08:33,543 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-02_01-08-33.log] [testng] 01:08:33,544 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b0c73f5 - End of configuration. [testng] [2025-01-02 01:08:33,682] [pool-1-thread-11] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc: [testng] 01:08:33,682 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:08:33,682 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:08:33,683 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-02_01-08-33.log] [testng] 01:08:33,684 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2db3a58 - End of configuration. [testng] [2025-01-02 01:08:33,842] [pool-1-thread-10] Initializing /data/strand/Series1_A.mrc: [testng] 01:08:33,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:08:33,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:08:33,844 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-02_01-08-33.log] [testng] 01:08:33,845 |-INFO in ch.qos.logback.core.sift.SiftProcessor@422dc32f - End of configuration. [testng] [2025-01-02 01:08:33,983] [pool-1-thread-9] Initializing /data/samples/1160.mrc: [testng] 01:08:33,983 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:08:33,984 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:08:33,984 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-02_01-08-33.log] [testng] 01:08:33,985 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b1076e3 - End of configuration. [testng] [2025-01-02 01:08:34,203] [pool-1-thread-8] Initializing /data/ascb/514_9903.mrc: [testng] 01:08:34,204 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:08:34,204 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:08:34,204 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-02_01-08-34.log] [testng] 01:08:34,205 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79bc10b8 - End of configuration. [testng] [2025-01-02 01:08:35,166] [pool-1-thread-7] Initializing /data/jcb/thyl-apr23-4.rec: [testng] 01:08:35,166 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:08:35,166 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:08:35,168 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-02_01-08-35.log] [testng] 01:08:35,168 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a19f1cf - End of configuration. [testng] [2025-01-02 01:08:36,428] [pool-1-thread-6] Initializing /data/ticket-10073/wtjoin4.rec: [testng] 01:08:36,429 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:08:36,429 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:08:36,430 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-02_01-08-36.log] [testng] 01:08:36,430 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d9006ce - End of configuration. [testng] [2025-01-02 01:08:36,574] [pool-1-thread-5] Initializing /data/ascb/c191ali.mrc: [testng] 01:08:36,575 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:08:36,575 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:08:36,576 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-02_01-08-36.log] [testng] 01:08:36,576 |-INFO in ch.qos.logback.core.sift.SiftProcessor@748b43a3 - End of configuration. [testng] [2025-01-02 01:08:36,782] [pool-1-thread-4] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: [testng] 01:08:36,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:08:36,783 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:08:36,783 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-02_01-08-36.log] [testng] 01:08:36,784 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b37b149 - End of configuration. [testng] [2025-01-02 01:08:36,948] [pool-1-thread-3] Initializing /data/bioformats2raw-198/test_uint8.mrc: [testng] 01:08:36,948 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:08:36,948 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:08:36,949 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-02_01-08-36.log] [testng] 01:08:36,950 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9fe5918 - End of configuration. [testng] [2025-01-02 01:08:37,087] [pool-1-thread-2] Initializing /data/dan/two.mrc: [testng] 01:08:37,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:08:37,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:08:37,088 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-02_01-08-37.log] [testng] 01:08:37,088 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b7a5201 - End of configuration. [testng] [2025-01-02 01:08:40,094] [pool-1-thread-3] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: [testng] [2025-01-02 01:08:40,256] [pool-1-thread-7] Initializing /data/ascb/c191.st: [testng] [2025-01-02 01:08:40,411] [pool-1-thread-4] Initializing /data/samples/golgi.mrc: [testng] [2025-01-02 01:08:40,650] [pool-1-thread-5] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc: [testng] [2025-01-02 01:08:40,820] [pool-1-thread-1] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: [testng] [2025-01-02 01:08:41,590] [pool-1-thread-12] Initializing /data/jcb/thylakoid5.rec: [testng] [2025-01-02 01:08:41,893] [pool-1-thread-2] Initializing /data/dan/three.mrc: [testng] [2025-01-02 01:08:42,095] [pool-1-thread-6] Initializing /data/ascb/cfa1071.mrc: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1060, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 24 seconds Finished: SUCCESS