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Started by upstream project "BIOFORMATS-test-repo" build number 214 originally caused by: Started by upstream project "Trigger" build number 241 originally caused by: Started by user devspace 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/jenkins12451780039497040317.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_34002_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] 10:07:23,612 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 10:07:23,614 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 10:07:23,614 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:07:23,614 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:07:23,615 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 10:07:23,615 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 10:07:23,616 |-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] 10:07:23,616 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:07:23,616 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:07:23,617 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 10:07:23,617 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 10:07:23,617 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 10:07:23,787 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 10:07:23,787 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 10:07:23,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 10:07:23,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 10:07:23,825 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 10:07:23,825 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 10:07:23,825 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 10:07:23,826 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 10:07:23,826 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 10:07:23,827 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 10:07:23,827 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 211 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-08 10:07:23,840] [main] java.version = 11.0.16 [testng] 10:07:23,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 10:07:23,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:07:23,908 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-08_10-07-23.log] [testng] 10:07:23,910 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-08 10:07:23,913] [main] testng.directory = /data [testng] [2024-10-08 10:07:23,913] [main] testng.configDirectory = /config [testng] [2024-10-08 10:07:23,927] [main] testng.multiplier = 1.0 [testng] [2024-10-08 10:07:23,928] [main] testng.in-memory = false [testng] [2024-10-08 10:07:23,929] [main] testng.allow-missing = false [testng] [2024-10-08 10:07:23,929] [main] user.language = en [testng] [2024-10-08 10:07:23,929] [main] user.country = ${user.country} [testng] [2024-10-08 10:07:23,929] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-08 10:07:52,832] [main] ---------------------------------------- [testng] [2024-10-08 10:07:52,832] [main] Total files: 46 [testng] [2024-10-08 10:07:52,832] [main] Scan time: 28.903 s (628 ms/file) [testng] [2024-10-08 10:07:52,832] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-08 10:09:03,658] [pool-1-thread-1] Initializing /data/imagesc-84715/working.vws: [testng] 10:09:03,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 10:09:03,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:09:03,661 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-08_10-09-03.log] [testng] 10:09:03,661 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7eb42bf - End of configuration. [testng] [2024-10-08 10:09:04,748] [pool-1-thread-12] Initializing /data/andreas/090812E4.vws: [testng] 10:09:04,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 10:09:04,749 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:09:04,750 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-08_10-09-04.log] [testng] 10:09:04,750 |-INFO in ch.qos.logback.core.sift.SiftProcessor@123a601f - End of configuration. [testng] [2024-10-08 10:09:07,374] [pool-1-thread-11] Initializing /data/andreas/090811E1.vws: [testng] 10:09:07,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 10:09:07,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:09:07,375 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-08_10-09-07.log] [testng] 10:09:07,376 |-INFO in ch.qos.logback.core.sift.SiftProcessor@260903aa - End of configuration. [testng] [2024-10-08 10:09:14,818] [pool-1-thread-10] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] 10:09:14,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 10:09:14,819 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:09:14,820 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-08_10-09-14.log] [testng] 10:09:14,820 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22e9269 - End of configuration. [testng] [2024-10-08 10:09:15,799] [pool-1-thread-9] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] 10:09:15,799 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 10:09:15,799 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:09:15,800 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-08_10-09-15.log] [testng] 10:09:15,800 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6522fb08 - End of configuration. [testng] [2024-10-08 10:09:16,932] [pool-1-thread-8] Initializing /data/samples/fibre.vws: [testng] 10:09:16,932 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 10:09:16,932 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:09:16,933 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-08_10-09-16.log] [testng] 10:09:16,933 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e1e360c - End of configuration. [testng] [2024-10-08 10:09:17,726] [pool-1-thread-7] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] 10:09:17,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 10:09:17,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:09:17,727 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-08_10-09-17.log] [testng] 10:09:17,727 |-INFO in ch.qos.logback.core.sift.SiftProcessor@525738bb - End of configuration. [testng] [2024-10-08 10:09:21,861] [pool-1-thread-6] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws: [testng] 10:09:21,861 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 10:09:21,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:09:21,863 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-08_10-09-21.log] [testng] 10:09:21,864 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2aead771 - End of configuration. [testng] [2024-10-08 10:09:23,208] [pool-1-thread-5] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] 10:09:23,209 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 10:09:23,209 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:09:23,209 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-08_10-09-23.log] [testng] 10:09:23,210 |-INFO in ch.qos.logback.core.sift.SiftProcessor@714f91da - End of configuration. [testng] [2024-10-08 10:09:26,246] [pool-1-thread-4] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws: [testng] 10:09:26,246 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 10:09:26,246 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:09:26,247 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-08_10-09-26.log] [testng] 10:09:26,247 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63433986 - End of configuration. [testng] [2024-10-08 10:09:28,030] [pool-1-thread-3] Initializing /data/imagesc-84715/not working.vws: [testng] 10:09:28,030 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 10:09:28,030 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:09:28,031 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-08_10-09-28.log] [testng] 10:09:28,031 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a237670 - End of configuration. [testng] [2024-10-08 10:09:29,143] [pool-1-thread-2] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] 10:09:29,144 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 10:09:29,144 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:09:29,145 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-08_10-09-29.log] [testng] 10:09:29,145 |-INFO in ch.qos.logback.core.sift.SiftProcessor@595f955 - End of configuration. [testng] [2024-10-08 10:09:45,096] [pool-1-thread-8] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] [2024-10-08 10:09:50,025] [pool-1-thread-5] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] [2024-10-08 10:10:08,370] [pool-1-thread-5] Initializing /data/gerhard/test.vws: [testng] [2024-10-08 10:10:17,206] [pool-1-thread-3] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws: [testng] [2024-10-08 10:10:20,521] [pool-1-thread-5] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] [2024-10-08 10:10:23,581] [pool-1-thread-8] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] [2024-10-08 10:10:30,517] [pool-1-thread-9] Initializing /data/stephan/two sequences.vws: [testng] [2024-10-08 10:10:31,900] [pool-1-thread-1] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] [2024-10-08 10:10:38,507] [pool-1-thread-5] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] [2024-10-08 10:10:49,673] [pool-1-thread-1] Initializing /data/christian/080807epi/080807epi2.vws: [testng] [2024-10-08 10:10:50,728] [pool-1-thread-10] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] [2024-10-08 10:11:13,025] [pool-1-thread-8] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws: [testng] [2024-10-08 10:11:17,312] [pool-1-thread-3] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] 11:09:07,585 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:09:07,585 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:09:07,586 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-08_11-09-07.log] [testng] 11:09:07,586 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4195105b - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1325, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 61 minutes 54 seconds Finished: SUCCESS