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Started by upstream project "BIOFORMATS-test-repo" build number 187 originally caused by: Started by upstream project "Trigger" build number 209 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/jenkins16700442127179300823.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_29634_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 test-automated: [testng] File leak detector installed [testng] 02:52:04,497 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:52:04,498 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 02:52:04,498 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:52:04,500 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:52:04,500 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:52:04,500 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:52:04,500 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:52:04,500 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:52:04,501 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:52:04,501 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:52:04,501 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:52:04,501 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:52:04,764 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:52:04,764 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:52:04,794 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:52:04,794 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:52:04,803 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:52:04,803 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:52:04,804 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:52:04,804 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:52:04,804 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 02:52:04,805 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 02:52:04,805 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 304 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-13 02:52:04,816] [main] java.version = 1.8.0_342 [testng] 02:52:04,819 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:52:04,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:52:04,869 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-13_02-52-04.log] [testng] 02:52:04,871 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-09-13 02:52:04,873] [main] testng.directory = /data [testng] [2024-09-13 02:52:04,874] [main] testng.configDirectory = /config [testng] [2024-09-13 02:52:04,915] [main] testng.multiplier = 1.0 [testng] [2024-09-13 02:52:04,915] [main] testng.in-memory = false [testng] [2024-09-13 02:52:04,915] [main] testng.allow-missing = false [testng] [2024-09-13 02:52:04,915] [main] user.language = en [testng] [2024-09-13 02:52:04,915] [main] user.country = ${user.country} [testng] [2024-09-13 02:52:04,916] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-09-13 02:52:06,479] [main] ---------------------------------------- [testng] [2024-09-13 02:52:06,479] [main] Total files: 32 [testng] [2024-09-13 02:52:06,479] [main] Scan time: 1.563 s (48 ms/file) [testng] [2024-09-13 02:52:06,479] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-13 02:52:13,332] [pool-1-thread-1] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] 02:52:13,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:52:13,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:52:13,337 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-13_02-52-13.log] [testng] 02:52:13,339 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57fa73d - End of configuration. [testng] [2024-09-13 02:52:13,815] [pool-1-thread-12] Initializing /data/sylvain/2009-10-23 12hr 18min.tif: [testng] 02:52:13,815 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:52:13,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:52:13,817 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-13_02-52-13.log] [testng] 02:52:13,818 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b71e927 - End of configuration. [testng] [2024-09-13 02:52:14,381] [pool-1-thread-11] Initializing /data/qa-29459/bad.jpg: [testng] 02:52:14,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:52:14,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:52:14,386 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-13_02-52-14.log] [testng] 02:52:14,387 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52b706e3 - End of configuration. [testng] [2024-09-13 02:52:14,457] [pool-1-thread-10] Initializing /data/keith/PF020328saur v3.1sc: [testng] 02:52:14,457 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:52:14,457 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:52:14,459 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-13_02-52-14.log] [testng] 02:52:14,460 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e779e55 - End of configuration. [testng] [2024-09-13 02:52:14,532] [pool-1-thread-9] Initializing /data/samples/Criterion.1sc: [testng] 02:52:14,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:52:14,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:52:14,535 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-13_02-52-14.log] [testng] 02:52:14,537 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78629081 - End of configuration. [testng] [2024-09-13 02:52:14,832] [pool-1-thread-8] Initializing /data/geert/bad example1.1sc.jpg: [testng] 02:52:14,834 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:52:14,834 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:52:14,835 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-13_02-52-14.log] [testng] 02:52:14,836 |-INFO in ch.qos.logback.core.sift.SiftProcessor@131441e4 - End of configuration. [testng] [2024-09-13 02:52:14,925] [pool-1-thread-7] Initializing /data/geert/bad example1.1sc: [testng] 02:52:14,926 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:52:14,926 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:52:14,927 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-13_02-52-14.log] [testng] 02:52:14,928 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a51bac9 - End of configuration. [testng] [2024-09-13 02:52:15,085] [pool-1-thread-6] Initializing /data/qa-29469/bad2.1sc: [testng] 02:52:15,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:52:15,086 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:52:15,086 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-13_02-52-15.log] [testng] 02:52:15,087 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e709b57 - End of configuration. [testng] [2024-09-13 02:52:15,259] [pool-1-thread-5] Initializing /data/david/Opened in imageJ.tiff: [testng] 02:52:15,260 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:52:15,260 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:52:15,262 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-13_02-52-15.log] [testng] 02:52:15,263 |-INFO in ch.qos.logback.core.sift.SiftProcessor@283fe409 - End of configuration. [testng] [2024-09-13 02:52:15,533] [pool-1-thread-4] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] 02:52:15,534 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:52:15,534 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:52:15,536 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-13_02-52-15.log] [testng] 02:52:15,537 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a1a7f46 - End of configuration. [testng] [2024-09-13 02:52:15,720] [pool-1-thread-3] Initializing /data/david/Original Biorad Gel format file.1sc: [testng] 02:52:15,721 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:52:15,721 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:52:15,722 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-13_02-52-15.log] [testng] 02:52:15,722 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43906dd8 - End of configuration. [testng] [2024-09-13 02:52:15,869] [pool-1-thread-2] Initializing /data/adrian/test_img.1sc: [testng] 02:52:15,869 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:52:15,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:52:15,871 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-13_02-52-15.log] [testng] 02:52:15,872 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f600fde - End of configuration. [testng] [2024-09-13 02:52:19,241] [pool-1-thread-11] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] [2024-09-13 02:52:19,699] [pool-1-thread-10] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] [2024-09-13 02:52:20,095] [pool-1-thread-3] Initializing /data/sylvain/2009-10-26 14hr 59min: [testng] [2024-09-13 02:52:20,316] [pool-1-thread-2] Initializing /data/geert/bad example1.jpg: [testng] [2024-09-13 02:52:20,412] [pool-1-thread-8] Initializing /data/qa-29459/bad.1sc: [testng] [2024-09-13 02:52:20,761] [pool-1-thread-5] Initializing /data/samples/imagesEight.1sc: [testng] [2024-09-13 02:52:20,807] [pool-1-thread-9] Initializing /data/keith/pg020410saur3.1sc: [testng] [2024-09-13 02:52:20,877] [pool-1-thread-6] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] [2024-09-13 02:52:20,982] [pool-1-thread-4] Initializing /data/qa-29469/bad3.1sc: [testng] [2024-09-13 02:52:21,136] [pool-1-thread-7] Initializing /data/geert/good example1.1sc: [testng] [2024-09-13 02:52:21,570] [pool-1-thread-12] Initializing /data/qa-16880/c-src v7.1sc: [testng] [2024-09-13 02:52:22,048] [pool-1-thread-1] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [testng] [2024-09-13 02:52:22,442] [pool-1-thread-9] Initializing /data/keith/test.1sc: [testng] [2024-09-13 02:52:22,738] [pool-1-thread-5] Initializing /data/geert/good example1.1sc.jpg: [testng] [2024-09-13 02:52:23,303] [pool-1-thread-6] Initializing /data/keith/test2.1sc: [testng] [2024-09-13 02:52:23,369] [pool-1-thread-3] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] [2024-09-13 02:52:23,487] [pool-1-thread-2] Initializing /data/keith/PF020426MRSA v2.1sc: [testng] [2024-09-13 02:52:23,530] [pool-1-thread-8] Initializing /data/qa-29469/good.1sc: [testng] [2024-09-13 02:52:23,651] [pool-1-thread-4] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] [2024-09-13 02:52:23,847] [pool-1-thread-9] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1696, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 24 seconds Finished: SUCCESS