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Started by upstream project "BIOFORMATS-test-repo" build number 28 originally caused by: Started by upstream project "Trigger" build number 31 originally caused by: Started by timer 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/jenkins2570108401166180695.sh + '[' leica-tcs = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_3723_merge_ci -v /uod/idr/repos/curated/leica-tcs:/data -v /uod/idr-scratch/merge-ci/curated/leica-tcs:/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] 02:31:44,219 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:31:44,221 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 02:31:44,221 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:31:44,222 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:31:44,223 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:31:44,223 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:31:44,223 |-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] 02:31:44,223 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:31:44,224 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:31:44,224 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:31:44,225 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:31:44,225 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:31:44,399 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:31:44,399 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:31:44,422 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:31:44,423 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:31:44,428 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:31:44,428 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:31:44,429 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:31:44,429 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:31:44,429 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 02:31:44,430 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 02:31:44,430 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 206 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-09 02:31:44,439] [main] java.version = 11.0.16 [testng] 02:31:44,443 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:31:44,443 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:31:44,486 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-09_02-31-44.log] [testng] 02:31:44,487 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-04-09 02:31:44,489] [main] testng.directory = /data [testng] [2024-04-09 02:31:44,489] [main] testng.configDirectory = /config [testng] [2024-04-09 02:31:44,501] [main] testng.multiplier = 1.0 [testng] [2024-04-09 02:31:44,502] [main] testng.in-memory = false [testng] [2024-04-09 02:31:44,502] [main] testng.allow-missing = false [testng] [2024-04-09 02:31:44,502] [main] user.language = en [testng] [2024-04-09 02:31:44,502] [main] user.country = ${user.country} [testng] [2024-04-09 02:31:44,502] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-04-09 02:31:56,055] [main] ---------------------------------------- [testng] [2024-04-09 02:31:56,055] [main] Total files: 944 [testng] [2024-04-09 02:31:56,055] [main] Scan time: 11.552 s (12 ms/file) [testng] [2024-04-09 02:31:56,055] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-09 02:32:29,482] [pool-1-thread-1] Initializing /data/stjude/AntoDay1cy3/c01f0001.TIF: [testng] 02:32:29,482 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:32:29,483 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:29,484 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-09_02-32-29.log] [testng] 02:32:29,485 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6700b805 - End of configuration. [testng] [2024-04-09 02:32:29,525] [pool-1-thread-12] Initializing /data/stjude/AntoDay4dblmy2GRP.tif: [testng] 02:32:29,525 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:32:29,525 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:29,526 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-09_02-32-29.log] [testng] 02:32:29,527 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3100407b - End of configuration. [testng] [2024-04-09 02:32:29,596] [pool-1-thread-11] Initializing /data/primate/Leica_Image.tif: [testng] 02:32:29,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:32:29,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:29,597 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-09_02-32-29.log] [testng] 02:32:29,597 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c1dea8 - End of configuration. [testng] [2024-04-09 02:32:29,660] [pool-1-thread-10] Initializing /data/stjude/AntoDay1dblGRP.tif: [testng] 02:32:29,660 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:32:29,660 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:29,661 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-09_02-32-29.log] [testng] 02:32:29,661 |-INFO in ch.qos.logback.core.sift.SiftProcessor@680f283a - End of configuration. [testng] [2024-04-09 02:32:29,691] [pool-1-thread-9] Initializing /data/brian/Series002_z01.tif: [testng] 02:32:29,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:32:29,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:29,691 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-09_02-32-29.log] [testng] 02:32:29,692 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b092899 - End of configuration. [testng] [2024-04-09 02:32:29,761] [pool-1-thread-8] Initializing /data/dave/series 35/042911_Series035_t00_z000_ch00.tif: [testng] 02:32:29,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:32:29,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:29,762 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-09_02-32-29.log] [testng] 02:32:29,762 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4161d894 - End of configuration. [testng] [2024-04-09 02:32:34,913] [pool-1-thread-7] Initializing /data/stjude/Antoday1dblcatsglGRP.tif: [testng] 02:32:34,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:32:34,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:34,914 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-09_02-32-34.log] [testng] 02:32:34,914 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7099abd7 - End of configuration. [testng] [2024-04-09 02:32:34,944] [pool-1-thread-6] Initializing /data/martin/Series028_z00_ch00.tif: [testng] 02:32:34,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:32:34,945 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:34,945 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-09_02-32-34.log] [testng] 02:32:34,945 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25fcc786 - End of configuration. [testng] [2024-04-09 02:32:34,981] [pool-1-thread-5] Initializing /data/stjude/Antoday1dblmysglGRP.tif: [testng] 02:32:34,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:32:34,982 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:34,982 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-09_02-32-34.log] [testng] 02:32:34,982 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55f8fc3c - End of configuration. [testng] [2024-04-09 02:32:35,021] [pool-1-thread-4] Initializing /data/brian/Series002_z00_ch00.tif: [testng] 02:32:35,021 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:32:35,021 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:35,023 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-09_02-32-35.log] [testng] 02:32:35,023 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69625148 - End of configuration. [testng] [2024-04-09 02:32:35,064] [pool-1-thread-3] Initializing /data/stjude/AntoDayzerocy3GRP.tif: [testng] 02:32:35,064 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:32:35,064 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:35,064 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-09_02-32-35.log] [testng] 02:32:35,065 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28b873ca - End of configuration. [testng] [2024-04-09 02:32:35,093] [pool-1-thread-2] Initializing /data/stjude/AntoDay4dblcatdataGRP.tif: [testng] 02:32:35,093 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:32:35,093 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:35,094 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-09_02-32-35.log] [testng] 02:32:35,094 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35027bb6 - End of configuration. [testng] [2024-04-09 02:32:37,176] [pool-1-thread-4] Initializing /data/stjude/AntoDay4dblmyGRP.tif: [testng] [2024-04-09 02:32:37,214] [pool-1-thread-11] Initializing /data/stjude/Antoday1dblcat2dataGRP.tif: [testng] [2024-04-09 02:32:37,244] [pool-1-thread-12] Initializing /data/stjude/AntoDayzerocy3OVP.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 795, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 10 minutes 18 seconds Finished: SUCCESS