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Started by upstream project "BIOFORMATS-test-repo" build number 3 originally caused by: Started by upstream project "Trigger" build number 4 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins17681992059383563362.sh + '[' jpeg2000 = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_454_merge_ci -v /uod/idr/repos/curated/jpeg2000:/data -v /uod/idr-scratch/merge-ci/curated/jpeg2000:/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] 02:32:24,197 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:32:24,198 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 02:32:24,199 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:32:24,199 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:32:24,200 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:32:24,200 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:32:24,201 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:32:24,201 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:32:24,201 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:32:24,202 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:32:24,202 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:32:24,202 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:32:24,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:32:24,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:32:24,399 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:32:24,399 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:32:24,405 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:32:24,405 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:32:24,405 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:32:24,405 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:32:24,405 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 02:32:24,407 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 02:32:24,407 |-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] [2024-03-16 02:32:24,416] [main] java.version = 11.0.16 [testng] 02:32:24,419 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:32:24,419 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:24,461 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-16_02-32-24.log] [testng] 02:32:24,462 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-03-16 02:32:24,465] [main] testng.directory = /data [testng] [2024-03-16 02:32:24,465] [main] testng.configDirectory = /config [testng] [2024-03-16 02:32:24,475] [main] testng.multiplier = 1.0 [testng] [2024-03-16 02:32:24,476] [main] testng.in-memory = false [testng] [2024-03-16 02:32:24,476] [main] testng.allow-missing = false [testng] [2024-03-16 02:32:24,476] [main] user.language = en [testng] [2024-03-16 02:32:24,476] [main] user.country = ${user.country} [testng] [2024-03-16 02:32:24,477] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-16 02:32:29,907] [main] ---------------------------------------- [testng] [2024-03-16 02:32:29,907] [main] Total files: 31 [testng] [2024-03-16 02:32:29,907] [main] Scan time: 5.43 s (175 ms/file) [testng] [2024-03-16 02:32:29,907] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 30 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-16 02:32:36,544] [pool-1-thread-1] Initializing /data/big-images/2kx2k.jpf: [testng] 02:32:36,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:32:36,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:36,546 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-16_02-32-36.log] [testng] 02:32:36,547 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41a29622 - End of configuration. [testng] [2024-03-16 02:32:36,668] [pool-1-thread-12] Initializing /data/misc/clown-rgb.jp2: [testng] 02:32:36,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:32:36,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:36,674 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-16_02-32-36.log] [testng] 02:32:36,675 |-INFO in ch.qos.logback.core.sift.SiftProcessor@542ab4c9 - End of configuration. [testng] [2024-03-16 02:32:36,793] [pool-1-thread-11] Initializing /data/vikram/Captured 4.jp2: [testng] 02:32:36,793 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:32:36,793 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:36,794 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-16_02-32-36.log] [testng] 02:32:36,795 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17ca5ee7 - End of configuration. [testng] [2024-03-16 02:32:36,961] [pool-1-thread-10] Initializing /data/misc/clown-rgb.jbig: [testng] 02:32:36,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:32:36,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:36,962 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-16_02-32-36.log] [testng] 02:32:36,962 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a9cc317 - End of configuration. [testng] [2024-03-16 02:32:37,303] [pool-1-thread-9] Initializing /data/david/multichannel-3d-MBF-type.jpx: [testng] 02:32:37,303 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:32:37,303 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:37,304 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-16_02-32-37.log] [testng] 02:32:37,305 |-INFO in ch.qos.logback.core.sift.SiftProcessor@80fad51 - End of configuration. [testng] [2024-03-16 02:32:38,056] [pool-1-thread-8] Initializing /data/mike/LCM-4-3-color-cleaned.tiff: [testng] 02:32:38,057 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:32:38,057 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:38,058 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-16_02-32-38.log] [testng] 02:32:38,058 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6748cb81 - End of configuration. [testng] [2024-03-16 02:32:38,385] [pool-1-thread-7] Initializing /data/david/cy5-tph.jp2: [testng] 02:32:38,386 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:32:38,386 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:38,387 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-16_02-32-38.log] [testng] 02:32:38,387 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3db161ea - End of configuration. [testng] [2024-03-16 02:32:38,603] [pool-1-thread-6] Initializing /data/david/000000_000001.jpx: [testng] 02:32:38,604 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:32:38,604 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:38,605 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-16_02-32-38.log] [testng] 02:32:38,605 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1fb5bf1 - End of configuration. [testng] [2024-03-16 02:32:38,812] [pool-1-thread-5] Initializing /data/david/multichannel-3d-non-MBF-trial-2.jpx: [testng] 02:32:38,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:32:38,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:38,814 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-16_02-32-38.log] [testng] 02:32:38,814 |-INFO in ch.qos.logback.core.sift.SiftProcessor@480db1ec - End of configuration. [testng] [2024-03-16 02:32:39,164] [pool-1-thread-4] Initializing /data/venu/Multichannel 3a.jpg: [testng] 02:32:39,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:32:39,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:39,165 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-16_02-32-39.log] [testng] 02:32:39,165 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19557c5 - End of configuration. [testng] [2024-03-16 02:32:39,231] [pool-1-thread-3] Initializing /data/mike/LCM-4-3-color-cleaned.jp2: [testng] 02:32:39,231 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:32:39,231 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:39,232 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-16_02-32-39.log] [testng] 02:32:39,232 |-INFO in ch.qos.logback.core.sift.SiftProcessor@427750bf - End of configuration. [testng] [2024-03-16 02:32:39,366] [pool-1-thread-2] Initializing /data/big-images/8kx8k.jpf: [testng] 02:32:39,366 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:32:39,366 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:39,367 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-16_02-32-39.log] [testng] 02:32:39,367 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1cc8b72f - End of configuration. [testng] [2024-03-16 02:32:42,256] [pool-1-thread-12] Initializing /data/venu/Multichannel 3.jp2: [testng] [2024-03-16 02:32:42,529] [pool-1-thread-4] Initializing /data/angel/002_L050071_32_01_09_x2.jp2: [testng] [2024-03-16 02:32:42,709] [pool-1-thread-10] Initializing /data/kraig/head.jp2: [testng] [2024-03-16 02:32:43,026] [pool-1-thread-11] Initializing /data/mario/b0bCDME-0007_wB05_s1_z1_t1_cGFP_u001.jp2: [testng] [2024-03-16 02:32:43,392] [pool-1-thread-8] Initializing /data/mike/LCM4-1-cr10-cleaned.jp2: [testng] [2024-03-16 02:32:45,295] [pool-1-thread-10] Initializing /data/angel/052_L050071_56_x2hv.jp2: [testng] [2024-03-16 02:32:47,827] [pool-1-thread-6] Initializing /data/vikram/Captured 5.jp2: [testng] [2024-03-16 02:32:49,678] [pool-1-thread-11] Initializing /data/misc/clown-rgb.jpc: [testng] [2024-03-16 02:32:49,899] [pool-1-thread-8] Initializing /data/big-images/4kx4k.jpf: [testng] [2024-03-16 02:32:50,064] [pool-1-thread-6] Initializing /data/aryeh/flour 12.jp2: [testng] [2024-03-16 02:32:51,204] [pool-1-thread-1] Initializing /data/david/multichannel-2d test-non MBF-type.jp2: [testng] [2024-03-16 02:32:51,409] [pool-1-thread-11] Initializing /data/david/multichannel-2d test.jp2: [testng] [2024-03-16 02:32:52,942] [pool-1-thread-6] Initializing /data/vikram/Captured 3.jp2: [testng] [2024-03-16 02:32:55,236] [pool-1-thread-3] Initializing /data/vikram/Captured 1.jp2: [testng] [2024-03-16 02:32:55,837] [pool-1-thread-6] Initializing /data/frans/flower.jp2: [testng] [2024-03-16 02:32:56,912] [pool-1-thread-12] Initializing /data/david/C1R1_FOS.jp2: [testng] [2024-03-16 02:32:57,144] [pool-1-thread-4] Initializing /data/mike/LCM-4-3-color-cleaned-LOCI.tiff: [testng] [2024-03-16 02:32:57,830] [pool-1-thread-3] Initializing /data/vikram/Captured 2.jp2: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1590, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 6 minutes 18 seconds Finished: SUCCESS