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Started by upstream project "BIOFORMATS-test-repo" build number 130 originally caused by: Started by upstream project "Trigger" build number 147 originally caused by: Started by user devspace 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/jenkins5540066924113212077.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_20383_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] 11:33:50,748 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 11:33:50,750 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 11:33:50,750 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:33:50,751 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:33:50,752 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 11:33:50,752 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 11:33:50,753 |-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] 11:33:50,753 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:33:50,753 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:33:50,754 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 11:33:50,754 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:33:50,754 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:33:50,928 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:33:50,928 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:33:50,950 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:33:50,950 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:33:50,956 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:33:50,956 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:33:50,956 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:33:50,956 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:33:50,957 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 11:33:50,957 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 11:33:50,957 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 204 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-23 11:33:50,966] [main] java.version = 11.0.16 [testng] 11:33:50,970 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:33:50,970 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:33:51,012 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-23_11-33-50.log] [testng] 11:33:51,014 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-07-23 11:33:51,016] [main] testng.directory = /data [testng] [2024-07-23 11:33:51,017] [main] testng.configDirectory = /config [testng] [2024-07-23 11:33:51,027] [main] testng.multiplier = 1.0 [testng] [2024-07-23 11:33:51,028] [main] testng.in-memory = false [testng] [2024-07-23 11:33:51,028] [main] testng.allow-missing = false [testng] [2024-07-23 11:33:51,028] [main] user.language = en [testng] [2024-07-23 11:33:51,028] [main] user.country = ${user.country} [testng] [2024-07-23 11:33:51,028] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-23 11:33:52,379] [main] ---------------------------------------- [testng] [2024-07-23 11:33:52,379] [main] Total files: 46 [testng] [2024-07-23 11:33:52,379] [main] Scan time: 1.35 s (29 ms/file) [testng] [2024-07-23 11:33:52,380] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-23 11:34:07,658] [pool-1-thread-1] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] 11:34:07,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 11:34:07,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:07,661 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-23_11-34-07.log] [testng] 11:34:07,661 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b5f6a96 - End of configuration. [testng] [2024-07-23 11:34:07,772] [pool-1-thread-12] Initializing /data/imagesc-84715/not working.vws: [testng] 11:34:07,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 11:34:07,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:07,773 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-23_11-34-07.log] [testng] 11:34:07,774 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c3b9b85 - End of configuration. [testng] [2024-07-23 11:34:07,921] [pool-1-thread-11] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws: [testng] 11:34:07,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 11:34:07,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:07,922 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-23_11-34-07.log] [testng] 11:34:07,922 |-INFO in ch.qos.logback.core.sift.SiftProcessor@776d92f3 - End of configuration. [testng] [2024-07-23 11:34:07,961] [pool-1-thread-10] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] 11:34:07,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 11:34:07,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:07,962 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-23_11-34-07.log] [testng] 11:34:07,962 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c80e05f - End of configuration. [testng] [2024-07-23 11:34:08,033] [pool-1-thread-9] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] 11:34:08,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 11:34:08,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:08,033 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-23_11-34-08.log] [testng] 11:34:08,034 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5da718ec - End of configuration. [testng] [2024-07-23 11:34:08,049] [pool-1-thread-8] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] 11:34:08,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 11:34:08,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:08,050 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-23_11-34-08.log] [testng] 11:34:08,050 |-INFO in ch.qos.logback.core.sift.SiftProcessor@411fd503 - End of configuration. [testng] [2024-07-23 11:34:08,103] [pool-1-thread-7] Initializing /data/gerhard/test.vws: [testng] 11:34:08,103 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 11:34:08,103 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:08,104 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-23_11-34-08.log] [testng] 11:34:08,104 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f7b8b80 - End of configuration. [testng] [2024-07-23 11:34:08,270] [pool-1-thread-6] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws: [testng] 11:34:08,270 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 11:34:08,270 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:08,271 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-23_11-34-08.log] [testng] 11:34:08,272 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fa78e24 - End of configuration. [testng] [2024-07-23 11:34:08,797] [pool-1-thread-5] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] 11:34:08,798 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 11:34:08,798 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:08,798 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-23_11-34-08.log] [testng] 11:34:08,799 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47a2f215 - End of configuration. [testng] [2024-07-23 11:34:11,802] [pool-1-thread-4] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] 11:34:11,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 11:34:11,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:11,803 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-23_11-34-11.log] [testng] 11:34:11,803 |-INFO in ch.qos.logback.core.sift.SiftProcessor@584036e9 - End of configuration. [testng] [2024-07-23 11:34:11,818] [pool-1-thread-3] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] 11:34:11,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 11:34:11,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:11,819 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-23_11-34-11.log] [testng] 11:34:11,819 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31df2777 - End of configuration. [testng] [2024-07-23 11:34:11,848] [pool-1-thread-2] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] 11:34:11,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 11:34:11,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:11,849 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-23_11-34-11.log] [testng] 11:34:11,850 |-INFO in ch.qos.logback.core.sift.SiftProcessor@205aaba5 - End of configuration. [testng] [2024-07-23 11:34:14,187] [pool-1-thread-3] Initializing /data/samples/fibre.vws: [testng] [2024-07-23 11:34:14,204] [pool-1-thread-2] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] [2024-07-23 11:34:14,230] [pool-1-thread-8] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] [2024-07-23 11:34:14,248] [pool-1-thread-9] Initializing /data/stephan/two sequences.vws: [testng] [2024-07-23 11:34:14,509] [pool-1-thread-11] Initializing /data/andreas/090811E1.vws: [testng] [2024-07-23 11:34:16,909] [pool-1-thread-10] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] [2024-07-23 11:34:17,238] [pool-1-thread-7] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] [2024-07-23 11:34:20,163] [pool-1-thread-4] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws: [testng] [2024-07-23 11:34:20,377] [pool-1-thread-3] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] [2024-07-23 11:34:21,685] [pool-1-thread-2] Initializing /data/christian/080807epi/080807epi2.vws: [testng] [2024-07-23 11:34:21,946] [pool-1-thread-8] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws: [testng] [2024-07-23 11:34:22,664] [pool-1-thread-1] Initializing /data/imagesc-84715/working.vws: [testng] [2024-07-23 11:34:23,020] [pool-1-thread-9] 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: 5 minutes 16 seconds Finished: SUCCESS