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Started by upstream project "BIOFORMATS-test-repo" build number 285 originally caused by: Started by upstream project "Trigger" build number 304 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins13358714781439916287.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_45063_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 -Duser.language=fr -Duser.country=FR 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 test-automated: [testng] File leak detector installed [testng] 03:45:14,211 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:45:14,212 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 03:45:14,212 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:45:14,213 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:45:14,213 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:45:14,214 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:45:14,214 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 03:45:14,214 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:45:14,214 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:45:14,215 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:45:14,215 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:45:14,215 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:45:14,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:45:14,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:45:14,462 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:45:14,462 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:45:14,469 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:45:14,469 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:45:14,469 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:45:14,470 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:45:14,470 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 03:45:14,471 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 03:45:14,471 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 257 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-09 03:45:14,480] [main] java.version = 1.8.0_342 [testng] 03:45:14,484 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:45:14,484 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:14,527 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-09_03-45-14.log] [testng] 03:45:14,529 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-09 03:45:14,530] [main] testng.directory = /data [testng] [2024-12-09 03:45:14,531] [main] testng.configDirectory = /config [testng] [2024-12-09 03:45:14,542] [main] testng.multiplier = 1.0 [testng] [2024-12-09 03:45:14,542] [main] testng.in-memory = false [testng] [2024-12-09 03:45:14,542] [main] testng.allow-missing = false [testng] [2024-12-09 03:45:14,542] [main] user.language = fr [testng] [2024-12-09 03:45:14,542] [main] user.country = FR [testng] [2024-12-09 03:45:14,543] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-09 03:45:16,653] [main] ---------------------------------------- [testng] [2024-12-09 03:45:16,653] [main] Total files: 32 [testng] [2024-12-09 03:45:16,653] [main] Scan time: 2.11 s (65 ms/file) [testng] [2024-12-09 03:45:16,653] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-09 03:45:33,251] [pool-1-thread-1] Initializing /data/samples/Criterion.1sc: [testng] 03:45:33,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:45:33,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:33,252 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-09_03-45-33.log] [testng] 03:45:33,253 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e3094f2 - End of configuration. [testng] [2024-12-09 03:45:33,549] [pool-1-thread-12] Initializing /data/keith/test.1sc: [testng] 03:45:33,550 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:45:33,550 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:33,550 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-09_03-45-33.log] [testng] 03:45:33,551 |-INFO in ch.qos.logback.core.sift.SiftProcessor@270816a3 - End of configuration. [testng] [2024-12-09 03:45:33,818] [pool-1-thread-11] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] 03:45:33,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:45:33,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:33,819 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-09_03-45-33.log] [testng] 03:45:33,819 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15dc516b - End of configuration. [testng] [2024-12-09 03:45:34,817] [pool-1-thread-10] Initializing /data/geert/bad example1.1sc.jpg: [testng] 03:45:34,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:45:34,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:34,818 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-09_03-45-34.log] [testng] 03:45:34,819 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4eece769 - End of configuration. [testng] [2024-12-09 03:45:34,949] [pool-1-thread-9] Initializing /data/samples/imagesEight.1sc: [testng] 03:45:34,949 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:45:34,949 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:34,950 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-09_03-45-34.log] [testng] 03:45:34,950 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5608b281 - End of configuration. [testng] [2024-12-09 03:45:35,181] [pool-1-thread-8] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] 03:45:35,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:45:35,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:35,182 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-09_03-45-35.log] [testng] 03:45:35,182 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26753d99 - End of configuration. [testng] [2024-12-09 03:45:35,466] [pool-1-thread-7] Initializing /data/keith/PF020328saur v3.1sc: [testng] 03:45:35,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:45:35,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:35,467 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-09_03-45-35.log] [testng] 03:45:35,467 |-INFO in ch.qos.logback.core.sift.SiftProcessor@70f62715 - End of configuration. [testng] [2024-12-09 03:45:35,726] [pool-1-thread-6] Initializing /data/sylvain/2009-10-26 14hr 59min: [testng] 03:45:35,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:45:35,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:35,727 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-09_03-45-35.log] [testng] 03:45:35,727 |-INFO in ch.qos.logback.core.sift.SiftProcessor@aa82368 - End of configuration. [testng] [2024-12-09 03:45:35,996] [pool-1-thread-5] Initializing /data/geert/bad example1.jpg: [testng] 03:45:35,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:45:35,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:35,997 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-09_03-45-35.log] [testng] 03:45:35,997 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f6a4905 - End of configuration. [testng] [2024-12-09 03:45:36,114] [pool-1-thread-4] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] 03:45:36,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:45:36,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:36,115 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-09_03-45-36.log] [testng] 03:45:36,115 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30cba11f - End of configuration. [testng] [2024-12-09 03:45:36,395] [pool-1-thread-3] Initializing /data/keith/test2.1sc: [testng] 03:45:36,395 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:45:36,395 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:36,396 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-09_03-45-36.log] [testng] 03:45:36,396 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f69ffab - End of configuration. [testng] [2024-12-09 03:45:36,688] [pool-1-thread-2] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] 03:45:36,688 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:45:36,688 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:36,688 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-09_03-45-36.log] [testng] 03:45:36,689 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30acc693 - End of configuration. [testng] [2024-12-09 03:45:41,152] [pool-1-thread-7] Initializing /data/qa-16880/c-src v7.1sc: [testng] [2024-12-09 03:45:41,491] [pool-1-thread-9] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] [2024-12-09 03:45:42,621] [pool-1-thread-3] Initializing /data/qa-29469/bad3.1sc: [testng] [2024-12-09 03:45:42,938] [pool-1-thread-12] Initializing /data/qa-29469/good.1sc: [testng] [2024-12-09 03:45:43,248] [pool-1-thread-5] Initializing /data/geert/good example1.1sc: [testng] [2024-12-09 03:45:43,584] [pool-1-thread-10] Initializing /data/adrian/test_img.1sc: [testng] [2024-12-09 03:45:43,896] [pool-1-thread-6] Initializing /data/keith/pg020410saur3.1sc: [testng] [2024-12-09 03:45:44,218] [pool-1-thread-4] Initializing /data/keith/PF020426MRSA v2.1sc: [testng] [2024-12-09 03:45:44,512] [pool-1-thread-8] Initializing /data/geert/bad example1.1sc: [testng] [2024-12-09 03:45:44,811] [pool-1-thread-1] Initializing /data/sylvain/2009-10-23 12hr 18min.tif: [testng] [2024-12-09 03:45:49,679] [pool-1-thread-6] Initializing /data/david/Original Biorad Gel format file.1sc: [testng] [2024-12-09 03:45:50,025] [pool-1-thread-4] Initializing /data/qa-29459/bad.jpg: [testng] [2024-12-09 03:45:50,275] [pool-1-thread-2] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] [2024-12-09 03:45:51,308] [pool-1-thread-11] Initializing /data/qa-29469/bad2.1sc: [testng] [2024-12-09 03:45:51,766] [pool-1-thread-7] Initializing /data/david/Opened in imageJ.tiff: [testng] [2024-12-09 03:45:52,751] [pool-1-thread-3] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [testng] [2024-12-09 03:45:54,002] [pool-1-thread-12] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] [2024-12-09 03:45:54,374] [pool-1-thread-8] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] [2024-12-09 03:45:54,709] [pool-1-thread-10] Initializing /data/geert/good example1.1sc.jpg: [testng] [2024-12-09 03:45:54,808] [pool-1-thread-5] Initializing /data/qa-29459/bad.1sc: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1696, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 49 seconds Finished: SUCCESS