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Started by upstream project "BIOFORMATS-test-repo" build number 193 originally caused by: Started by upstream project "Trigger" build number 215 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins1263972978081104805.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_30558_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings test-automated: [testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 01:43:59,786 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:43:59,788 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 01:43:59,788 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:43:59,789 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:43:59,789 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:43:59,789 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:43:59,790 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:43:59,790 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:43:59,790 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:43:59,791 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:43:59,791 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:43:59,791 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:43:59,957 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:43:59,957 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:43:59,982 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:43:59,983 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:43:59,989 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:43:59,989 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:43:59,989 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:43:59,990 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:43:59,990 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 01:43:59,991 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 01:43:59,991 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 201 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-19 01:44:00,000] [main] java.version = 21 [testng] 01:44:00,004 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:44:00,004 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:00,047 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-19_01-44-00.log] [testng] 01:44:00,048 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-09-19 01:44:00,050] [main] testng.directory = /data [testng] [2024-09-19 01:44:00,050] [main] testng.configDirectory = /config [testng] [2024-09-19 01:44:00,059] [main] testng.multiplier = 1.0 [testng] [2024-09-19 01:44:00,060] [main] testng.in-memory = false [testng] [2024-09-19 01:44:00,060] [main] testng.allow-missing = false [testng] [2024-09-19 01:44:00,060] [main] user.language = en [testng] [2024-09-19 01:44:00,060] [main] user.country = ${user.country} [testng] [2024-09-19 01:44:00,060] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-09-19 01:44:02,853] [main] ---------------------------------------- [testng] [2024-09-19 01:44:02,853] [main] Total files: 46 [testng] [2024-09-19 01:44:02,854] [main] Scan time: 2.793 s (60 ms/file) [testng] [2024-09-19 01:44:02,854] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-19 01:44:26,579] [pool-1-thread-1] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] 01:44:26,580 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:44:26,580 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:26,582 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-19_01-44-26.log] [testng] 01:44:26,582 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e49e1d1 - End of configuration. [testng] [2024-09-19 01:44:26,728] [pool-1-thread-12] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] 01:44:26,728 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:44:26,728 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:26,729 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-19_01-44-26.log] [testng] 01:44:26,729 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3696316c - End of configuration. [testng] [2024-09-19 01:44:30,279] [pool-1-thread-11] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws: [testng] 01:44:30,279 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:44:30,279 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:30,281 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-19_01-44-30.log] [testng] 01:44:30,281 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63f4ebb0 - End of configuration. [testng] [2024-09-19 01:44:30,974] [pool-1-thread-10] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] 01:44:30,974 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:44:30,974 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:30,975 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-19_01-44-30.log] [testng] 01:44:30,975 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a20652f - End of configuration. [testng] [2024-09-19 01:44:31,066] [pool-1-thread-9] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] 01:44:31,066 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:44:31,066 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:31,066 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-19_01-44-31.log] [testng] 01:44:31,067 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11bb4551 - End of configuration. [testng] [2024-09-19 01:44:32,578] [pool-1-thread-8] Initializing /data/christian/080807epi/080807epi2.vws: [testng] 01:44:32,578 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:44:32,579 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:32,579 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-19_01-44-32.log] [testng] 01:44:32,580 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2eaf757a - End of configuration. [testng] [2024-09-19 01:44:32,651] [pool-1-thread-7] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] 01:44:32,651 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:44:32,651 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:32,652 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-19_01-44-32.log] [testng] 01:44:32,652 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58ffd31b - End of configuration. [testng] [2024-09-19 01:44:32,863] [pool-1-thread-6] Initializing /data/gerhard/test.vws: [testng] 01:44:32,863 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:44:32,863 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:32,864 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-19_01-44-32.log] [testng] 01:44:32,864 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e2e5006 - End of configuration. [testng] [2024-09-19 01:44:33,001] [pool-1-thread-5] Initializing /data/andreas/090811E1.vws: [testng] 01:44:33,001 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:44:33,001 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:33,002 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-19_01-44-33.log] [testng] 01:44:33,002 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25e0d02c - End of configuration. [testng] [2024-09-19 01:44:35,701] [pool-1-thread-4] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] 01:44:35,701 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:44:35,701 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:35,702 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-19_01-44-35.log] [testng] 01:44:35,702 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a4f9280 - End of configuration. [testng] [2024-09-19 01:44:35,727] [pool-1-thread-3] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] 01:44:35,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:44:35,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:35,728 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-19_01-44-35.log] [testng] 01:44:35,728 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f2a0562 - End of configuration. [testng] [2024-09-19 01:44:35,746] [pool-1-thread-2] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws: [testng] 01:44:35,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:44:35,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:35,747 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-19_01-44-35.log] [testng] 01:44:35,747 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c8e7878 - End of configuration. [testng] [2024-09-19 01:44:38,382] [pool-1-thread-10] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws: [testng] [2024-09-19 01:44:38,832] [pool-1-thread-3] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] [2024-09-19 01:44:38,943] [pool-1-thread-8] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] [2024-09-19 01:44:42,545] [pool-1-thread-6] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] [2024-09-19 01:44:42,942] [pool-1-thread-4] Initializing /data/imagesc-84715/working.vws: [testng] [2024-09-19 01:44:43,768] [pool-1-thread-1] Initializing /data/imagesc-84715/not working.vws: [testng] [2024-09-19 01:44:43,950] [pool-1-thread-6] Initializing /data/stephan/two sequences.vws: [testng] [2024-09-19 01:44:44,314] [pool-1-thread-7] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] [2024-09-19 01:44:44,651] [pool-1-thread-3] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] [2024-09-19 01:44:44,809] [pool-1-thread-10] Initializing /data/samples/fibre.vws: [testng] [2024-09-19 01:44:45,113] [pool-1-thread-7] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] [2024-09-19 01:44:45,281] [pool-1-thread-10] Initializing /data/andreas/090812E4.vws: [testng] [2024-09-19 01:44:46,349] [pool-1-thread-3] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.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 52 seconds Finished: SUCCESS