Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins7031622606362311422.sh + '[' imaris = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_44270_merge_ci -v /uod/idr/repos/curated/imaris:/data -v /uod/idr-scratch/merge-ci/curated/imaris:/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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 10:55:09,019 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 10:55:09,021 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 10:55:09,021 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:55:09,022 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:55:09,022 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 10:55:09,023 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 10:55:09,023 |-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] 10:55:09,023 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:55:09,023 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:55:09,024 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 10:55:09,024 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 10:55:09,024 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 10:55:09,233 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 10:55:09,233 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 10:55:09,257 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 10:55:09,257 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 10:55:09,324 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 10:55:09,324 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 10:55:09,324 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 10:55:09,324 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 10:55:09,324 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 10:55:09,325 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 10:55:09,325 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 302 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-05 10:55:09,334] [main] java.version = 21 [testng] 10:55:09,337 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 10:55:09,337 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:55:09,434 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-05_10-55-09.log] [testng] 10:55:09,435 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-12-05 10:55:09,440] [main] testng.directory = /data [testng] [2024-12-05 10:55:09,441] [main] testng.configDirectory = /config [testng] [2024-12-05 10:55:09,682] [main] testng.multiplier = 1.0 [testng] [2024-12-05 10:55:09,683] [main] testng.in-memory = false [testng] [2024-12-05 10:55:09,684] [main] testng.allow-missing = false [testng] [2024-12-05 10:55:09,684] [main] user.language = en [testng] [2024-12-05 10:55:09,684] [main] user.country = ${user.country} [testng] [2024-12-05 10:55:09,684] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-05 10:55:19,366] [main] ---------------------------------------- [testng] [2024-12-05 10:55:19,366] [main] Total files: 73 [testng] [2024-12-05 10:55:19,366] [main] Scan time: 9.682 s (132 ms/file) [testng] [2024-12-05 10:55:19,367] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 63 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-05 10:55:37,128] [pool-1-thread-1] Initializing /data/public/eliana/2016-07-26_17.11.03_Sample Prefix_5P298C2_Protocol.ims: [testng] 10:55:37,128 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 10:55:37,128 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:55:37,129 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-05_10-55-37.log] [testng] 10:55:37,130 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ae4034 - End of configuration. [testng] [2024-12-05 10:55:37,216] [pool-1-thread-12] Initializing /data/qa-17515/Organoid=1.ims: [testng] 10:55:37,216 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 10:55:37,216 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:55:37,217 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-05_10-55-37.log] [testng] 10:55:37,217 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a972fbd - End of configuration. [testng] [2024-12-05 10:55:37,313] [pool-1-thread-11] Initializing /data/public/davemason/Convallaria_3C_10T_confocal_IMS3.ims: [testng] 10:55:37,313 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 10:55:37,313 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:55:37,314 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-05_10-55-37.log] [testng] 10:55:37,315 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2749d8f - End of configuration. [testng] [2024-12-05 10:55:37,384] [pool-1-thread-10] Initializing /data/qa-4898/o383_1_457_CS_r1.ims: [testng] 10:55:37,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 10:55:37,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:55:37,385 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-05_10-55-37.log] [testng] 10:55:37,385 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2895e1b0 - End of configuration. [testng] [2024-12-05 10:55:37,446] [pool-1-thread-9] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal_deconvolved.ims: [testng] 10:55:37,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 10:55:37,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:55:37,447 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-05_10-55-37.log] [testng] 10:55:37,448 |-INFO in ch.qos.logback.core.sift.SiftProcessor@723950d2 - End of configuration. [testng] [2024-12-05 10:55:37,497] [pool-1-thread-8] Initializing /data/generated/10-31_E_t0010.ims: [testng] 10:55:37,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 10:55:37,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:55:37,498 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-05_10-55-37.log] [testng] 10:55:37,498 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6de672d0 - End of configuration. [testng] [2024-12-05 10:55:37,527] [pool-1-thread-7] Initializing /data/public/davemason/Convallaria_3C_3T_2x2grid_confocal.ims: [testng] 10:55:37,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 10:55:37,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:55:37,528 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-05_10-55-37.log] [testng] 10:55:37,529 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c0d7c0b - End of configuration. [testng] [2024-12-05 10:55:37,589] [pool-1-thread-6] Initializing /data/jason/imaris_5_5_demoimages/PlantCell.ims: [testng] 10:55:37,589 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 10:55:37,589 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:55:37,590 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-05_10-55-37.log] [testng] 10:55:37,590 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76a327cd - End of configuration. [testng] [2024-12-05 10:55:37,651] [pool-1-thread-5] Initializing /data/generated/10-31_E_t0014.ims: [testng] 10:55:37,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 10:55:37,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:55:37,652 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-05_10-55-37.log] [testng] 10:55:37,653 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d9382e2 - End of configuration. [testng] [2024-12-05 10:55:37,676] [pool-1-thread-4] Initializing /data/oliver/Stack2_u16Bit.ims: [testng] 10:55:37,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 10:55:37,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:55:37,677 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-05_10-55-37.log] [testng] 10:55:37,678 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2cdd2468 - End of configuration. [testng] [2024-12-05 10:55:37,739] [pool-1-thread-3] Initializing /data/public/bitplane/lz4/croppedRetinaLz4.ims: [testng] 10:55:37,739 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 10:55:37,739 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:55:37,740 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-05_10-55-37.log] [testng] 10:55:37,740 |-INFO in ch.qos.logback.core.sift.SiftProcessor@617b72d7 - End of configuration. [testng] [2024-12-05 10:55:37,825] [pool-1-thread-2] Initializing /data/jason/imaris_5_5_demoimages/retina.ims: [testng] 10:55:37,825 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 10:55:37,825 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:55:37,826 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-05_10-55-37.log] [testng] 10:55:37,827 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1bf816e0 - End of configuration. BUILD SUCCESSFUL Total time: 1 minute 56 seconds Finished: SUCCESS