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Started by upstream project "BIOFORMATS-test-repo" build number 42 originally caused by: Started by upstream project "Trigger" build number 49 originally caused by: Started by user devspace 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/jenkins883245567220324983.sh + '[' gatan-dm2 = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_5943_merge_ci -v /uod/idr/repos/curated/gatan-dm2:/data -v /uod/idr-scratch/merge-ci/curated/gatan-dm2:/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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 06:31:41,345 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 06:31:41,347 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 06:31:41,347 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:31:41,348 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:31:41,349 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 06:31:41,349 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 06:31:41,349 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 06:31:41,349 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:31:41,350 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:31:41,350 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 06:31:41,351 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 06:31:41,351 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 06:31:41,529 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 06:31:41,529 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 06:31:41,558 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 06:31:41,558 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 06:31:41,564 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 06:31:41,564 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 06:31:41,564 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 06:31:41,565 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 06:31:41,565 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 06:31:41,566 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 06:31:41,566 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 216 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-23 06:31:41,576] [main] java.version = 11.0.16 [testng] 06:31:41,579 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 06:31:41,579 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:31:41,623 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-23_06-31-41.log] [testng] 06:31:41,625 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-04-23 06:31:41,627] [main] testng.directory = /data [testng] [2024-04-23 06:31:41,627] [main] testng.configDirectory = /config [testng] [2024-04-23 06:31:41,638] [main] testng.multiplier = 1.0 [testng] [2024-04-23 06:31:41,640] [main] testng.in-memory = false [testng] [2024-04-23 06:31:41,640] [main] testng.allow-missing = false [testng] [2024-04-23 06:31:41,640] [main] user.language = en [testng] [2024-04-23 06:31:41,640] [main] user.country = ${user.country} [testng] [2024-04-23 06:31:41,640] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-04-23 06:31:42,548] [main] ---------------------------------------- [testng] [2024-04-23 06:31:42,548] [main] Total files: 25 [testng] [2024-04-23 06:31:42,548] [main] Scan time: 0.908 s (36 ms/file) [testng] [2024-04-23 06:31:42,548] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 18 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-23 06:31:43,524] [pool-1-thread-1] Initializing /data/imagic/not read correctly/Abeta Moon_preview.png: [testng] 06:31:43,524 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 06:31:43,525 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:31:43,526 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-23_06-31-43.log] [testng] 06:31:43,527 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e17b77a - End of configuration. [testng] [2024-04-23 06:31:43,539] [pool-1-thread-12] Initializing /data/imagic/not read correctly/Zucchini_preview.png: [testng] 06:31:43,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 06:31:43,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:31:43,541 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-23_06-31-43.log] [testng] 06:31:43,541 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28a44680 - End of configuration. [testng] [2024-04-23 06:31:43,550] [pool-1-thread-11] Initializing /data/imagic/Histiocyte in Skin Dermis.dm2: [testng] 06:31:43,550 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 06:31:43,550 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:31:43,551 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-23_06-31-43.log] [testng] 06:31:43,552 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14fbb192 - End of configuration. [testng] [2024-04-23 06:31:43,572] [pool-1-thread-10] Initializing /data/pang/screen capture of metadata/tem_dm_keywords_info.png: [testng] 06:31:43,572 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 06:31:43,572 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:31:43,573 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-23_06-31-43.log] [testng] 06:31:43,573 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d39b66d - End of configuration. [testng] [2024-04-23 06:31:43,578] [pool-1-thread-9] Initializing /data/imagic/1-1.dm2: [testng] 06:31:43,579 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 06:31:43,579 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:31:43,579 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-23_06-31-43.log] [testng] 06:31:43,580 |-INFO in ch.qos.logback.core.sift.SiftProcessor@390a5c3a - End of configuration. [testng] [2024-04-23 06:31:43,597] [pool-1-thread-8] Initializing /data/pang/signed: [testng] 06:31:43,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 06:31:43,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:31:43,599 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-23_06-31-43.log] [testng] 06:31:43,599 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43043779 - End of configuration. [testng] [2024-04-23 06:31:43,614] [pool-1-thread-7] Initializing /data/pang/screen capture of metadata/tem_dm_microscope_info.png: [testng] 06:31:43,615 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 06:31:43,615 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:31:43,616 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-23_06-31-43.log] [testng] 06:31:43,616 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67100144 - End of configuration. [testng] [2024-04-23 06:31:43,622] [pool-1-thread-6] Initializing /data/pang/unproc-auto: [testng] 06:31:43,622 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 06:31:43,622 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:31:43,623 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-23_06-31-43.log] [testng] 06:31:43,624 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25cfda94 - End of configuration. [testng] [2024-04-23 06:31:43,636] [pool-1-thread-5] Initializing /data/pang/screen capture of metadata/tem_dm_tags_info1.png: [testng] 06:31:43,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 06:31:43,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:31:43,637 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-23_06-31-43.log] [testng] 06:31:43,638 |-INFO in ch.qos.logback.core.sift.SiftProcessor@182319d1 - End of configuration. [testng] [2024-04-23 06:31:43,643] [pool-1-thread-4] Initializing /data/imagic/TEM 10118.dm2: [testng] 06:31:43,643 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 06:31:43,643 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:31:43,644 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-23_06-31-43.log] [testng] 06:31:43,645 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6854e89b - End of configuration. [testng] [2024-04-23 06:31:43,659] [pool-1-thread-3] Initializing /data/pang/DLMeD2E1_010500x03.dm2: [testng] 06:31:43,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 06:31:43,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:31:43,660 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-23_06-31-43.log] [testng] 06:31:43,660 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dd7dd74 - End of configuration. [testng] [2024-04-23 06:31:43,677] [pool-1-thread-2] Initializing /data/imagic/not read correctly/Abeta Moon.dm2: [testng] 06:31:43,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 06:31:43,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:31:43,678 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-23_06-31-43.log] [testng] 06:31:43,678 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57616645 - End of configuration. [testng] [2024-04-23 06:31:45,259] [pool-1-thread-2] Initializing /data/imagic/not read correctly/Zucchini.dm2: [testng] [2024-04-23 06:31:45,269] [pool-1-thread-5] Initializing /data/pang/grating025k.dm2: [testng] [2024-04-23 06:31:45,278] [pool-1-thread-7] Initializing /data/pang/10500x-o4: [testng] [2024-04-23 06:31:45,294] [pool-1-thread-10] Initializing /data/pang/screen capture of metadata/tem_dm_general_info.png: [testng] [2024-04-23 06:31:45,297] [pool-1-thread-8] Initializing /data/imagic/13008.dm2: [testng] [2024-04-23 06:31:45,313] [pool-1-thread-6] Initializing /data/pang/screen capture of metadata/tem_dm_tags_info2.png: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 954, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 8 seconds Finished: SUCCESS