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Started by upstream project "BIOFORMATS-test-repo" build number 235 originally caused by: Started by upstream project "Trigger" build number 260 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/jenkins14645038548721234936.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_36990_merge_ci -v /uod/idr/repos/curated/biorad-gel:/data -v /uod/idr-scratch/merge-ci/curated/biorad-gel:/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] 04:31:43,002 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 04:31:43,004 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 04:31:43,004 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:31:43,005 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:31:43,005 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 04:31:43,006 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 04:31:43,006 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 04:31:43,006 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:31:43,007 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:31:43,007 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 04:31:43,007 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 04:31:43,008 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 04:31:43,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 04:31:43,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 04:31:43,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 04:31:43,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 04:31:43,203 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 04:31:43,203 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 04:31:43,203 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 04:31:43,203 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 04:31:43,204 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 04:31:43,204 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 04:31:43,204 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 197 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-26 04:31:43,213] [main] java.version = 11.0.16 [testng] 04:31:43,216 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:31:43,216 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:31:43,258 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-26_04-31-43.log] [testng] 04:31:43,259 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-26 04:31:43,261] [main] testng.directory = /data [testng] [2024-10-26 04:31:43,261] [main] testng.configDirectory = /config [testng] [2024-10-26 04:31:43,270] [main] testng.multiplier = 1.0 [testng] [2024-10-26 04:31:43,272] [main] testng.in-memory = false [testng] [2024-10-26 04:31:43,272] [main] testng.allow-missing = false [testng] [2024-10-26 04:31:43,272] [main] user.language = en [testng] [2024-10-26 04:31:43,272] [main] user.country = ${user.country} [testng] [2024-10-26 04:31:43,272] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-26 04:31:55,644] [main] ---------------------------------------- [testng] [2024-10-26 04:31:55,644] [main] Total files: 32 [testng] [2024-10-26 04:31:55,644] [main] Scan time: 12.372 s (386 ms/file) [testng] [2024-10-26 04:31:55,644] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-26 04:32:38,972] [pool-1-thread-1] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] 04:32:38,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 04:32:38,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:38,974 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-26_04-32-38.log] [testng] 04:32:38,975 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c768f4d - End of configuration. [testng] [2024-10-26 04:32:40,153] [pool-1-thread-12] Initializing /data/keith/test.1sc: [testng] 04:32:40,153 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 04:32:40,153 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:40,154 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-26_04-32-40.log] [testng] 04:32:40,155 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79504da7 - End of configuration. [testng] [2024-10-26 04:32:40,509] [pool-1-thread-11] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [testng] 04:32:40,509 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 04:32:40,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:40,510 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-26_04-32-40.log] [testng] 04:32:40,511 |-INFO in ch.qos.logback.core.sift.SiftProcessor@162e8f69 - End of configuration. [testng] [2024-10-26 04:32:41,721] [pool-1-thread-10] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] 04:32:41,721 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 04:32:41,721 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:41,721 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-26_04-32-41.log] [testng] 04:32:41,722 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a0512b4 - End of configuration. [testng] [2024-10-26 04:32:42,109] [pool-1-thread-9] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] 04:32:42,109 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 04:32:42,109 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:42,110 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-26_04-32-42.log] [testng] 04:32:42,110 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5221f142 - End of configuration. [testng] [2024-10-26 04:32:42,446] [pool-1-thread-8] Initializing /data/samples/Criterion.1sc: [testng] 04:32:42,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 04:32:42,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:42,447 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-26_04-32-42.log] [testng] 04:32:42,447 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1321b722 - End of configuration. [testng] [2024-10-26 04:32:42,767] [pool-1-thread-7] Initializing /data/david/Original Biorad Gel format file.1sc: [testng] 04:32:42,767 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 04:32:42,767 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:42,768 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-26_04-32-42.log] [testng] 04:32:42,768 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6842797b - End of configuration. [testng] [2024-10-26 04:32:43,106] [pool-1-thread-6] Initializing /data/david/Opened in imageJ.tiff: [testng] 04:32:43,106 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:32:43,106 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:43,107 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-26_04-32-43.log] [testng] 04:32:43,107 |-INFO in ch.qos.logback.core.sift.SiftProcessor@703fe27b - End of configuration. [testng] [2024-10-26 04:32:44,277] [pool-1-thread-5] Initializing /data/adrian/test_img.1sc: [testng] 04:32:44,277 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 04:32:44,277 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:44,277 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-26_04-32-44.log] [testng] 04:32:44,278 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29dd5535 - End of configuration. [testng] [2024-10-26 04:32:44,562] [pool-1-thread-4] Initializing /data/qa-29469/bad2.1sc: [testng] 04:32:44,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 04:32:44,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:44,563 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-26_04-32-44.log] [testng] 04:32:44,564 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a8d6f7d - End of configuration. [testng] [2024-10-26 04:32:44,945] [pool-1-thread-3] Initializing /data/sylvain/2009-10-23 12hr 18min.tif: [testng] 04:32:44,945 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 04:32:44,945 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:44,946 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-26_04-32-44.log] [testng] 04:32:44,946 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a3788d6 - End of configuration. [testng] [2024-10-26 04:32:46,175] [pool-1-thread-2] Initializing /data/qa-29459/bad.1sc: [testng] 04:32:46,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:32:46,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:46,176 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-26_04-32-46.log] [testng] 04:32:46,176 |-INFO in ch.qos.logback.core.sift.SiftProcessor@400c7a3d - End of configuration. [testng] [2024-10-26 04:32:50,918] [pool-1-thread-12] Initializing /data/geert/good example1.1sc: [testng] [2024-10-26 04:32:51,257] [pool-1-thread-7] Initializing /data/geert/bad example1.1sc: [testng] [2024-10-26 04:32:51,668] [pool-1-thread-2] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] [2024-10-26 04:32:52,006] [pool-1-thread-8] Initializing /data/qa-16880/c-src v7.1sc: [testng] [2024-10-26 04:32:52,387] [pool-1-thread-4] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] [2024-10-26 04:32:53,529] [pool-1-thread-5] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] [2024-10-26 04:32:54,697] [pool-1-thread-9] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] [2024-10-26 04:32:55,855] [pool-1-thread-10] Initializing /data/keith/PF020426MRSA v2.1sc: [testng] [2024-10-26 04:32:59,279] [pool-1-thread-10] Initializing /data/keith/pg020410saur3.1sc: [testng] [2024-10-26 04:32:59,763] [pool-1-thread-8] Initializing /data/qa-29459/bad.jpg: [testng] [2024-10-26 04:33:00,040] [pool-1-thread-7] Initializing /data/keith/PF020328saur v3.1sc: [testng] [2024-10-26 04:33:00,422] [pool-1-thread-1] Initializing /data/geert/good example1.1sc.jpg: [testng] [2024-10-26 04:33:00,536] [pool-1-thread-6] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] [2024-10-26 04:33:00,899] [pool-1-thread-12] Initializing /data/keith/test2.1sc: [testng] [2024-10-26 04:33:01,222] [pool-1-thread-2] Initializing /data/qa-29469/bad3.1sc: [testng] [2024-10-26 04:33:01,627] [pool-1-thread-11] Initializing /data/samples/imagesEight.1sc: [testng] [2024-10-26 04:33:02,059] [pool-1-thread-3] Initializing /data/geert/bad example1.1sc.jpg: [testng] [2024-10-26 04:33:04,204] [pool-1-thread-10] Initializing /data/geert/bad example1.jpg: [testng] [2024-10-26 04:33:04,631] [pool-1-thread-7] Initializing /data/qa-29469/good.1sc: [testng] [2024-10-26 04:33:05,107] [pool-1-thread-12] Initializing /data/sylvain/2009-10-26 14hr 59min: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1696, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 1 minute 28 seconds Finished: SUCCESS