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Started by upstream project "BIOFORMATS-test-repo" build number 263 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins2330152395333178174.sh + '[' cellomics = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_41552_merge_ci -v /uod/idr/repos/curated/cellomics:/data -v /uod/idr-scratch/merge-ci/curated/cellomics:/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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 18:20:09,463 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 18:20:09,464 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 18:20:09,464 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 18:20:09,465 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 18:20:09,466 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 18:20:09,466 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 18:20:09,467 |-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] 18:20:09,467 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 18:20:09,467 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 18:20:09,468 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 18:20:09,468 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 18:20:09,468 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 18:20:09,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 18:20:09,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 18:20:09,658 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 18:20:09,658 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 18:20:09,665 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 18:20:09,665 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 18:20:09,665 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 18:20:09,665 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 18:20:09,666 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 18:20:09,666 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 18:20:09,666 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 199 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-21 18:20:09,676] [main] java.version = 21 [testng] 18:20:09,679 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 18:20:09,679 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 18:20:09,722 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-21_18-20-09.log] [testng] 18:20:09,723 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-11-21 18:20:09,725] [main] testng.directory = /data [testng] [2024-11-21 18:20:09,725] [main] testng.configDirectory = /config [testng] [2024-11-21 18:20:09,734] [main] testng.multiplier = 1.0 [testng] [2024-11-21 18:20:09,734] [main] testng.in-memory = false [testng] [2024-11-21 18:20:09,734] [main] testng.allow-missing = false [testng] [2024-11-21 18:20:09,734] [main] user.language = en [testng] [2024-11-21 18:20:09,735] [main] user.country = ${user.country} [testng] [2024-11-21 18:20:09,735] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-21 18:20:47,841] [main] ---------------------------------------- [testng] [2024-11-21 18:20:47,841] [main] Total files: 2539 [testng] [2024-11-21 18:20:47,842] [main] Scan time: 38.106 s (15 ms/file) [testng] [2024-11-21 18:20:47,842] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-21 18:21:25,844] [pool-1-thread-1] Initializing /data/johannes/MFGTMP_081222130005_E07f00d0.C01: [testng] 18:21:25,845 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 18:21:25,845 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 18:21:25,846 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-21_18-21-25.log] [testng] 18:21:25,847 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d393911 - End of configuration. [testng] [2024-11-21 18:21:26,583] [pool-1-thread-12] Initializing /data/johannes/MFGTMP_081128200001_A02f239d1.C01: [testng] 18:21:26,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 18:21:26,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 18:21:26,584 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-21_18-21-26.log] [testng] 18:21:26,585 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62dce629 - End of configuration. [testng] [2024-11-21 18:21:27,375] [pool-1-thread-11] Initializing /data/samples/sparse-plate/plate_E03f00d0.C01: [testng] 18:21:27,375 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 18:21:27,375 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 18:21:27,376 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-21_18-21-27.log] [testng] 18:21:27,376 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a506c95 - End of configuration. [testng] [2024-11-21 18:21:28,153] [pool-1-thread-10] Initializing /data/public/BBBC001/AS_09125_050118150001_A03f00d0.DIB: [testng] 18:21:28,153 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 18:21:28,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 18:21:28,154 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-21_18-21-28.log] [testng] 18:21:28,155 |-INFO in ch.qos.logback.core.sift.SiftProcessor@477bcf96 - End of configuration. [testng] [2024-11-21 18:21:28,836] [pool-1-thread-9] Initializing /data/omar/FB03f00o1.C01: [testng] 18:21:28,837 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 18:21:28,837 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 18:21:28,837 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-21_18-21-28.log] [testng] 18:21:28,838 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12ff2bdf - End of configuration. [testng] [2024-11-21 18:21:29,479] [pool-1-thread-8] Initializing /data/omar/FB03f00d0.C01: [testng] 18:21:29,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 18:21:29,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 18:21:29,480 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-21_18-21-29.log] [testng] 18:21:29,480 |-INFO in ch.qos.logback.core.sift.SiftProcessor@723df018 - End of configuration. [testng] [2024-11-21 18:21:30,027] [pool-1-thread-7] Initializing /data/samples/different-field-count/plate_B03f00d0.C01: [testng] 18:21:30,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 18:21:30,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 18:21:30,028 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-21_18-21-30.log] [testng] 18:21:30,028 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5dca484a - End of configuration. [testng] [2024-11-21 18:21:30,503] [pool-1-thread-6] Initializing /data/omar/FB03f00d1.C01: [testng] 18:21:30,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 18:21:30,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 18:21:30,504 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-21_18-21-30.log] [testng] 18:21:30,504 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27dd0921 - End of configuration. [testng] [2024-11-21 18:21:31,072] [pool-1-thread-5] Initializing /data/qa-7352/test/MFGTMP-PC_130509120002_B02f00d0.C01: [testng] 18:21:31,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 18:21:31,072 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 18:21:31,073 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-21_18-21-31.log] [testng] 18:21:31,073 |-INFO in ch.qos.logback.core.sift.SiftProcessor@473fe167 - End of configuration. [testng] [2024-11-21 18:21:31,738] [pool-1-thread-4] Initializing /data/qa-21720/AS_09125_050117190001_A14f00d0.DIB: [testng] 18:21:31,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 18:21:31,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 18:21:31,739 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-21_18-21-31.log] [testng] 18:21:31,739 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75d92581 - End of configuration. [testng] [2024-11-21 18:21:32,284] [pool-1-thread-3] Initializing /data/samples/plate-size/plate_B03f00d0.C01: [testng] 18:21:32,284 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 18:21:32,284 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 18:21:32,285 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-21_18-21-32.log] [testng] 18:21:32,285 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5569168c - End of configuration. [testng] [2024-11-21 18:21:32,871] [pool-1-thread-2] Initializing /data/omar/FB03f03o2.DIB: [testng] 18:21:32,871 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 18:21:32,871 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 18:21:32,872 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-21_18-21-32.log] [testng] 18:21:32,872 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d582384 - End of configuration. [testng] [2024-11-21 18:21:39,219] [pool-1-thread-2] Initializing /data/omar/FB03f00o2.C01: [testng] [2024-11-21 18:21:43,076] [pool-1-thread-1] Initializing /data/lee/icd002235_090127090001_a01f00d1.c01: [testng] [2024-11-21 18:21:43,836] [pool-1-thread-9] Initializing /data/harri/MFGTMP-PC_111018140003/MFGTMP-PC_111018140003_E04f00d0.C01: [testng] [2024-11-21 18:21:44,595] [pool-1-thread-12] Initializing /data/qa-7352/test/MFGTMP-PC_130509120002_B02f00o1.C01: [testng] [2024-11-21 18:21:45,289] [pool-1-thread-6] Initializing /data/lee/AS_09125_050116030001_D03f00d0.DIB: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 901, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 46 minutes 2 seconds Finished: SUCCESS