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Started by upstream project "BIOFORMATS-test-repo" build number 23 originally caused by: Started by upstream project "Trigger" build number 26 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins6749320940189568009.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_2834_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 test-automated: [testng] File leak detector installed [testng] 01:43:57,430 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:43:57,433 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 01:43:57,433 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:43:57,435 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:43:57,436 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:43:57,436 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:43:57,436 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:43:57,436 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:43:57,437 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:43:57,438 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:43:57,438 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:43:57,438 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:43:57,708 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:43:57,708 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:43:57,747 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:43:57,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:43:57,758 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:43:57,758 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:43:57,758 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:43:57,759 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:43:57,759 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 01:43:57,760 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 01:43:57,760 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 323 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-05 01:43:57,771] [main] java.version = 1.8.0_342 [testng] 01:43:57,776 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:43:57,776 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:57,831 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-05_01-43-57.log] [testng] 01:43:57,833 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-04-05 01:43:57,835] [main] testng.directory = /data [testng] [2024-04-05 01:43:57,835] [main] testng.configDirectory = /config [testng] [2024-04-05 01:43:57,849] [main] testng.multiplier = 1.0 [testng] [2024-04-05 01:43:57,849] [main] testng.in-memory = false [testng] [2024-04-05 01:43:57,850] [main] testng.allow-missing = false [testng] [2024-04-05 01:43:57,850] [main] user.language = en [testng] [2024-04-05 01:43:57,850] [main] user.country = ${user.country} [testng] [2024-04-05 01:43:57,850] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-04-05 01:43:59,560] [main] ---------------------------------------- [testng] [2024-04-05 01:43:59,560] [main] Total files: 46 [testng] [2024-04-05 01:43:59,560] [main] Scan time: 1.71 s (37 ms/file) [testng] [2024-04-05 01:43:59,561] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-05 01:44:18,816] [pool-1-thread-1] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] 01:44:18,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:44:18,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:18,818 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-05_01-44-18.log] [testng] 01:44:18,819 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61db72b3 - End of configuration. [testng] [2024-04-05 01:44:18,956] [pool-1-thread-12] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] 01:44:18,956 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:44:18,956 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:18,957 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-05_01-44-18.log] [testng] 01:44:18,958 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c261851 - End of configuration. [testng] [2024-04-05 01:44:22,695] [pool-1-thread-11] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] 01:44:22,696 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:44:22,696 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:22,697 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-05_01-44-22.log] [testng] 01:44:22,698 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2424e7d2 - End of configuration. [testng] [2024-04-05 01:44:22,751] [pool-1-thread-10] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] 01:44:22,751 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:44:22,751 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:22,752 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-05_01-44-22.log] [testng] 01:44:22,752 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ae17bb4 - End of configuration. [testng] [2024-04-05 01:44:22,765] [pool-1-thread-9] Initializing /data/stephan/two sequences.vws: [testng] 01:44:22,765 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:44:22,766 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:22,766 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-05_01-44-22.log] [testng] 01:44:22,766 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ab1d2fb - End of configuration. [testng] [2024-04-05 01:44:22,784] [pool-1-thread-8] Initializing /data/samples/fibre.vws: [testng] 01:44:22,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:44:22,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:22,785 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-05_01-44-22.log] [testng] 01:44:22,785 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72e69056 - End of configuration. [testng] [2024-04-05 01:44:22,807] [pool-1-thread-7] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws: [testng] 01:44:22,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:44:22,808 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:22,808 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-05_01-44-22.log] [testng] 01:44:22,809 |-INFO in ch.qos.logback.core.sift.SiftProcessor@db201bb - End of configuration. [testng] [2024-04-05 01:44:22,847] [pool-1-thread-6] Initializing /data/imagesc-84715/not working.vws: [testng] 01:44:22,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:44:22,848 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:22,848 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-05_01-44-22.log] [testng] 01:44:22,849 |-INFO in ch.qos.logback.core.sift.SiftProcessor@173cb9af - End of configuration. [testng] [2024-04-05 01:44:23,032] [pool-1-thread-5] Initializing /data/andreas/090811E1.vws: [testng] 01:44:23,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:44:23,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:23,032 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-05_01-44-23.log] [testng] 01:44:23,033 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77450173 - End of configuration. [testng] [2024-04-05 01:44:25,794] [pool-1-thread-4] Initializing /data/christian/080807epi/080807epi2.vws: [testng] 01:44:25,795 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:44:25,795 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:25,796 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-05_01-44-25.log] [testng] 01:44:25,796 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e5094df - End of configuration. [testng] [2024-04-05 01:44:25,873] [pool-1-thread-3] Initializing /data/imagesc-84715/working.vws: [testng] 01:44:25,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:44:25,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:25,874 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-05_01-44-25.log] [testng] 01:44:25,874 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71f29009 - End of configuration. [testng] [2024-04-05 01:44:26,314] [pool-1-thread-2] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] 01:44:26,315 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:44:26,315 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:26,315 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-05_01-44-26.log] [testng] 01:44:26,316 |-INFO in ch.qos.logback.core.sift.SiftProcessor@284a4f24 - End of configuration. [testng] [2024-04-05 01:44:28,317] [pool-1-thread-11] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] [2024-04-05 01:44:31,956] [pool-1-thread-8] Initializing /data/andreas/090812E4.vws: [testng] [2024-04-05 01:44:32,957] [pool-1-thread-2] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws: [testng] [2024-04-05 01:44:33,724] [pool-1-thread-10] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] [2024-04-05 01:44:34,189] [pool-1-thread-4] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] [2024-04-05 01:44:34,300] [pool-1-thread-9] Initializing /data/gerhard/test.vws: [testng] [2024-04-05 01:44:34,659] [pool-1-thread-1] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] [2024-04-05 01:44:34,926] [pool-1-thread-4] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] [2024-04-05 01:44:35,522] [pool-1-thread-1] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] [2024-04-05 01:44:37,113] [pool-1-thread-10] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] [2024-04-05 01:44:37,277] [pool-1-thread-7] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws: [testng] [2024-04-05 01:44:37,578] [pool-1-thread-9] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] [2024-04-05 01:44:37,904] [pool-1-thread-6] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.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 3 seconds Finished: SUCCESS