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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@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins6543317782819255201.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_36930_merge_ci -v /uod/idr/repos/curated/tillvision:/data -v /uod/idr-scratch/merge-ci/curated/tillvision:/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] 02:40:14,632 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:40:14,634 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 02:40:14,634 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:40:14,635 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:40:14,636 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:40:14,636 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:40:14,637 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:40:14,637 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:40:14,637 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:40:14,638 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:40:14,638 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:40:14,638 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:40:14,819 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:40:14,819 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:40:14,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:40:14,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:40:14,850 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:40:14,850 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:40:14,850 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:40:14,850 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:40:14,850 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 02:40:14,851 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 02:40:14,851 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 214 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-26 02:40:14,861] [main] java.version = 11.0.16 [testng] 02:40:14,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:40:14,865 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:14,910 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-26_02-40-14.log] [testng] 02:40:14,911 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-26 02:40:14,913] [main] testng.directory = /data [testng] [2024-10-26 02:40:14,914] [main] testng.configDirectory = /config [testng] [2024-10-26 02:40:14,924] [main] testng.multiplier = 1.0 [testng] [2024-10-26 02:40:14,925] [main] testng.in-memory = false [testng] [2024-10-26 02:40:14,925] [main] testng.allow-missing = false [testng] [2024-10-26 02:40:14,926] [main] user.language = en [testng] [2024-10-26 02:40:14,926] [main] user.country = ${user.country} [testng] [2024-10-26 02:40:14,926] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-26 02:40:33,018] [main] ---------------------------------------- [testng] [2024-10-26 02:40:33,018] [main] Total files: 46 [testng] [2024-10-26 02:40:33,018] [main] Scan time: 18.092 s (393 ms/file) [testng] [2024-10-26 02:40:33,019] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-26 02:41:19,812] [pool-1-thread-1] Initializing /data/imagesc-84715/working.vws: [testng] 02:41:19,812 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:41:19,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:19,814 |-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_02-41-19.log] [testng] 02:41:19,815 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b56f962 - End of configuration. [testng] [2024-10-26 02:41:20,624] [pool-1-thread-12] Initializing /data/andreas/090812E4.vws: [testng] 02:41:20,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:41:20,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:20,626 |-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_02-41-20.log] [testng] 02:41:20,627 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e4390d3 - End of configuration. [testng] [2024-10-26 02:41:22,620] [pool-1-thread-11] Initializing /data/andreas/090811E1.vws: [testng] 02:41:22,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:41:22,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:22,621 |-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_02-41-22.log] [testng] 02:41:22,621 |-INFO in ch.qos.logback.core.sift.SiftProcessor@520170f - End of configuration. [testng] [2024-10-26 02:41:27,918] [pool-1-thread-10] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] 02:41:27,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:41:27,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:27,919 |-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_02-41-27.log] [testng] 02:41:27,920 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fe4ccdb - End of configuration. [testng] [2024-10-26 02:41:28,411] [pool-1-thread-9] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] 02:41:28,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:41:28,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:28,413 |-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_02-41-28.log] [testng] 02:41:28,413 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58921827 - End of configuration. [testng] [2024-10-26 02:41:29,160] [pool-1-thread-8] Initializing /data/samples/fibre.vws: [testng] 02:41:29,160 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:41:29,160 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:29,161 |-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_02-41-29.log] [testng] 02:41:29,161 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11028e96 - End of configuration. [testng] [2024-10-26 02:41:29,543] [pool-1-thread-7] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] 02:41:29,543 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:41:29,543 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:29,544 |-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_02-41-29.log] [testng] 02:41:29,544 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3696316c - End of configuration. [testng] [2024-10-26 02:41:35,172] [pool-1-thread-6] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws: [testng] 02:41:35,172 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:41:35,172 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:35,173 |-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_02-41-35.log] [testng] 02:41:35,174 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41b76a90 - End of configuration. [testng] [2024-10-26 02:41:35,974] [pool-1-thread-5] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] 02:41:35,974 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:41:35,974 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:35,975 |-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_02-41-35.log] [testng] 02:41:35,975 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63f4ebb0 - End of configuration. [testng] [2024-10-26 02:41:37,523] [pool-1-thread-4] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws: [testng] 02:41:37,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:41:37,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:37,523 |-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_02-41-37.log] [testng] 02:41:37,524 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1fdb7478 - End of configuration. [testng] [2024-10-26 02:41:38,726] [pool-1-thread-3] Initializing /data/imagesc-84715/not working.vws: [testng] 02:41:38,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:41:38,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:38,727 |-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_02-41-38.log] [testng] 02:41:38,728 |-INFO in ch.qos.logback.core.sift.SiftProcessor@498df528 - End of configuration. [testng] [2024-10-26 02:41:39,338] [pool-1-thread-2] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] 02:41:39,338 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:41:39,338 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:39,339 |-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_02-41-39.log] [testng] 02:41:39,340 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e10125b - End of configuration. [testng] [2024-10-26 02:41:51,133] [pool-1-thread-8] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] [2024-10-26 02:41:53,761] [pool-1-thread-5] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] [2024-10-26 02:42:05,758] [pool-1-thread-5] Initializing /data/gerhard/test.vws: [testng] [2024-10-26 02:42:13,127] [pool-1-thread-3] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws: [testng] [2024-10-26 02:42:15,153] [pool-1-thread-5] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] [2024-10-26 02:42:17,315] [pool-1-thread-8] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] [2024-10-26 02:42:22,699] [pool-1-thread-9] Initializing /data/stephan/two sequences.vws: [testng] [2024-10-26 02:42:23,806] [pool-1-thread-1] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] [2024-10-26 02:42:28,550] [pool-1-thread-5] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] [2024-10-26 02:42:38,197] [pool-1-thread-1] Initializing /data/christian/080807epi/080807epi2.vws: [testng] [2024-10-26 02:42:39,115] [pool-1-thread-10] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] [2024-10-26 02:42:59,985] [pool-1-thread-8] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws: [testng] [2024-10-26 02:43:05,306] [pool-1-thread-6] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1325, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 16 minutes 36 seconds Finished: SUCCESS