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Started by upstream project "BIOFORMATS-test-repo" build number 12 originally caused by: Started by upstream project "Trigger" build number 15 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/jenkins12511681219948418652.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_1848_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] 01:00:03,016 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:00:03,018 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 01:00:03,019 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:00:03,020 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:00:03,021 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:00:03,021 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:00:03,022 |-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] 01:00:03,022 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:00:03,023 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:00:03,024 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:00:03,024 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:00:03,024 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:00:03,259 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:00:03,259 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:00:03,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:00:03,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:00:03,304 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:00:03,305 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:00:03,305 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:00:03,305 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:00:03,305 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 01:00:03,307 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 01:00:03,307 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 284 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-26 01:00:03,320] [main] java.version = 11.0.16 [testng] 01:00:03,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:00:03,325 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:00:03,373 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-26_01-00-03.log] [testng] 01:00:03,376 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-03-26 01:00:03,378] [main] testng.directory = /data [testng] [2024-03-26 01:00:03,378] [main] testng.configDirectory = /config [testng] [2024-03-26 01:00:03,390] [main] testng.multiplier = 1.0 [testng] [2024-03-26 01:00:03,391] [main] testng.in-memory = false [testng] [2024-03-26 01:00:03,392] [main] testng.allow-missing = false [testng] [2024-03-26 01:00:03,392] [main] user.language = en [testng] [2024-03-26 01:00:03,392] [main] user.country = ${user.country} [testng] [2024-03-26 01:00:03,392] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-26 01:00:05,836] [main] ---------------------------------------- [testng] [2024-03-26 01:00:05,836] [main] Total files: 46 [testng] [2024-03-26 01:00:05,837] [main] Scan time: 2.444 s (53 ms/file) [testng] [2024-03-26 01:00:05,837] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-26 01:00:24,441] [pool-1-thread-1] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] 01:00:24,442 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:00:24,442 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:00:24,445 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-26_01-00-24.log] [testng] 01:00:24,446 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75864d01 - End of configuration. [testng] [2024-03-26 01:00:24,600] [pool-1-thread-12] Initializing /data/imagesc-84715/not working.vws: [testng] 01:00:24,600 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:00:24,600 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:00:24,602 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-26_01-00-24.log] [testng] 01:00:24,602 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b31582d - End of configuration. [testng] [2024-03-26 01:00:24,871] [pool-1-thread-11] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws: [testng] 01:00:24,871 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:00:24,871 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:00:24,872 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-26_01-00-24.log] [testng] 01:00:24,873 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22e9269 - End of configuration. [testng] [2024-03-26 01:00:24,933] [pool-1-thread-10] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] 01:00:24,934 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:00:24,934 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:00:24,935 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-26_01-00-24.log] [testng] 01:00:24,935 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7cb7be07 - End of configuration. [testng] [2024-03-26 01:00:25,199] [pool-1-thread-9] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] 01:00:25,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:00:25,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:00:25,200 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-26_01-00-25.log] [testng] 01:00:25,201 |-INFO in ch.qos.logback.core.sift.SiftProcessor@687c173d - End of configuration. [testng] [2024-03-26 01:00:25,227] [pool-1-thread-8] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] 01:00:25,227 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:00:25,227 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:00:25,228 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-26_01-00-25.log] [testng] 01:00:25,228 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f0c1e0 - End of configuration. [testng] [2024-03-26 01:00:25,471] [pool-1-thread-7] Initializing /data/gerhard/test.vws: [testng] 01:00:25,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:00:25,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:00:25,472 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-26_01-00-25.log] [testng] 01:00:25,472 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10d9881e - End of configuration. [testng] [2024-03-26 01:00:25,632] [pool-1-thread-6] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws: [testng] 01:00:25,632 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:00:25,632 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:00:25,633 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-26_01-00-25.log] [testng] 01:00:25,633 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37e2fb0c - End of configuration. [testng] [2024-03-26 01:00:26,255] [pool-1-thread-5] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] 01:00:26,256 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:00:26,256 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:00:26,257 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-26_01-00-26.log] [testng] 01:00:26,258 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d1fe317 - End of configuration. [testng] [2024-03-26 01:00:29,343] [pool-1-thread-4] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] 01:00:29,343 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:00:29,344 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:00:29,345 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-26_01-00-29.log] [testng] 01:00:29,345 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74675abb - End of configuration. [testng] [2024-03-26 01:00:29,384] [pool-1-thread-3] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] 01:00:29,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:00:29,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:00:29,385 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-26_01-00-29.log] [testng] 01:00:29,385 |-INFO in ch.qos.logback.core.sift.SiftProcessor@beb22b - End of configuration. [testng] [2024-03-26 01:00:29,619] [pool-1-thread-2] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] 01:00:29,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:00:29,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:00:29,620 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-26_01-00-29.log] [testng] 01:00:29,621 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c240398 - End of configuration. [testng] [2024-03-26 01:00:35,460] [pool-1-thread-2] Initializing /data/samples/fibre.vws: [testng] [2024-03-26 01:00:35,501] [pool-1-thread-8] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] [2024-03-26 01:00:35,701] [pool-1-thread-3] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] [2024-03-26 01:00:35,750] [pool-1-thread-7] Initializing /data/stephan/two sequences.vws: [testng] [2024-03-26 01:00:36,570] [pool-1-thread-10] Initializing /data/andreas/090811E1.vws: [testng] [2024-03-26 01:00:40,458] [pool-1-thread-2] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] [2024-03-26 01:00:40,883] [pool-1-thread-9] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] [2024-03-26 01:00:44,711] [pool-1-thread-8] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws: [testng] [2024-03-26 01:00:44,829] [pool-1-thread-12] Initializing /data/christian/080807epi/080807epi2.vws: [testng] [2024-03-26 01:00:44,987] [pool-1-thread-11] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] [2024-03-26 01:00:47,063] [pool-1-thread-3] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws: [testng] [2024-03-26 01:00:48,370] [pool-1-thread-4] Initializing /data/imagesc-84715/working.vws: [testng] [2024-03-26 01:00:48,994] [pool-1-thread-7] Initializing /data/andreas/090812E4.vws: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1325, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 6 minutes 10 seconds Finished: SUCCESS