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Started by upstream project "BIOFORMATS-test-repo" build number 254 originally caused by: Started by upstream project "Trigger" build number 278 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/jenkins4159442574480535230.sh + '[' mrc = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_40032_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] 00:54:47,976 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:54:47,978 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:54:47,978 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:54:47,979 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:54:47,979 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:54:47,980 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:54:47,980 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:54:47,980 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:54:47,981 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:54:47,982 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:54:47,982 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:54:47,983 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:54:48,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:54:48,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:54:48,179 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:54:48,179 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:54:48,186 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:54:48,186 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:54:48,186 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:54:48,186 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:54:48,187 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:54:48,188 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:54:48,188 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 207 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-13 00:54:48,197] [main] java.version = 17.0.2 [testng] 00:54:48,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:54:48,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:48,240 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-13_00-54-48.log] [testng] 00:54:48,241 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-11-13 00:54:48,243] [main] testng.directory = /data [testng] [2024-11-13 00:54:48,243] [main] testng.configDirectory = /config [testng] [2024-11-13 00:54:48,252] [main] testng.multiplier = 1.0 [testng] [2024-11-13 00:54:48,253] [main] testng.in-memory = false [testng] [2024-11-13 00:54:48,253] [main] testng.allow-missing = false [testng] [2024-11-13 00:54:48,253] [main] user.language = en [testng] [2024-11-13 00:54:48,253] [main] user.country = ${user.country} [testng] [2024-11-13 00:54:48,253] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-13 00:54:54,747] [main] ---------------------------------------- [testng] [2024-11-13 00:54:54,748] [main] Total files: 20 [testng] [2024-11-13 00:54:54,748] [main] Scan time: 6.494 s (324 ms/file) [testng] [2024-11-13 00:54:54,748] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-13 00:54:59,036] [pool-1-thread-1] Initializing /data/dan/one.mrc: [testng] 00:54:59,037 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:54:59,037 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:59,039 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-13_00-54-59.log] [testng] 00:54:59,039 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74b939a0 - End of configuration. [testng] [2024-11-13 00:54:59,245] [pool-1-thread-12] Initializing /data/samples/1160.mrc: [testng] 00:54:59,245 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:54:59,245 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:59,247 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-13_00-54-59.log] [testng] 00:54:59,247 |-INFO in ch.qos.logback.core.sift.SiftProcessor@417af931 - End of configuration. [testng] [2024-11-13 00:54:59,442] [pool-1-thread-11] Initializing /data/ascb/c191ali.mrc: [testng] 00:54:59,442 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:54:59,442 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:59,443 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-13_00-54-59.log] [testng] 00:54:59,443 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d2d12b8 - End of configuration. [testng] [2024-11-13 00:54:59,906] [pool-1-thread-10] Initializing /data/bioformats2raw-198/test_uint8.mrc: [testng] 00:54:59,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:54:59,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:54:59,908 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-13_00-54-59.log] [testng] 00:54:59,908 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6781dc87 - End of configuration. [testng] [2024-11-13 00:55:00,294] [pool-1-thread-9] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: [testng] 00:55:00,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:55:00,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:00,296 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-13_00-55-00.log] [testng] 00:55:00,296 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76110ba6 - End of configuration. [testng] [2024-11-13 00:55:00,509] [pool-1-thread-8] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc: [testng] 00:55:00,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:55:00,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:00,510 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-13_00-55-00.log] [testng] 00:55:00,511 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a2cce9f - End of configuration. [testng] [2024-11-13 00:55:00,741] [pool-1-thread-7] Initializing /data/jcb/thylakoid5.rec: [testng] 00:55:00,741 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:55:00,742 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:00,742 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-13_00-55-00.log] [testng] 00:55:00,743 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38577afe - End of configuration. [testng] [2024-11-13 00:55:01,125] [pool-1-thread-6] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: [testng] 00:55:01,126 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:55:01,126 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:01,126 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-13_00-55-01.log] [testng] 00:55:01,127 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f564c66 - End of configuration. [testng] [2024-11-13 00:55:01,588] [pool-1-thread-5] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: [testng] 00:55:01,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:55:01,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:01,589 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-13_00-55-01.log] [testng] 00:55:01,589 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1adfcd6f - End of configuration. [testng] [2024-11-13 00:55:01,817] [pool-1-thread-4] Initializing /data/dan/three.mrc: [testng] 00:55:01,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:55:01,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:01,818 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-13_00-55-01.log] [testng] 00:55:01,819 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6292a096 - End of configuration. [testng] [2024-11-13 00:55:02,046] [pool-1-thread-3] Initializing /data/ascb/cfa1071.mrc: [testng] 00:55:02,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:55:02,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:02,047 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-13_00-55-02.log] [testng] 00:55:02,047 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27442a3b - End of configuration. [testng] [2024-11-13 00:55:02,535] [pool-1-thread-2] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: [testng] 00:55:02,536 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:55:02,536 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:02,537 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-13_00-55-02.log] [testng] 00:55:02,537 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7fef34cf - End of configuration. [testng] [2024-11-13 00:55:06,446] [pool-1-thread-10] Initializing /data/ticket-10073/wtjoin4.rec: [testng] [2024-11-13 00:55:06,677] [pool-1-thread-2] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc: [testng] [2024-11-13 00:55:06,900] [pool-1-thread-5] Initializing /data/samples/golgi.mrc: [testng] [2024-11-13 00:55:07,256] [pool-1-thread-6] Initializing /data/ascb/c191.st: [testng] [2024-11-13 00:55:07,457] [pool-1-thread-9] Initializing /data/dan/two.mrc: [testng] [2024-11-13 00:55:07,669] [pool-1-thread-11] Initializing /data/ascb/514_9903.mrc: [testng] [2024-11-13 00:55:08,057] [pool-1-thread-7] Initializing /data/jcb/thyl-apr23-4.rec: [testng] [2024-11-13 00:55:08,502] [pool-1-thread-4] 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: 30 seconds Finished: SUCCESS