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Started by upstream project "BIOFORMATS-test-repo" build number 79 originally caused by: Started by upstream project "Trigger" build number 87 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/jenkins8265361437119321762.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_12019_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 01:45:17,676 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:45:17,678 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 01:45:17,678 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:45:17,679 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:45:17,680 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:45:17,681 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:45:17,681 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:45:17,681 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:45:17,682 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:45:17,683 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:45:17,683 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:45:17,684 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:45:17,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:45:17,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:45:17,899 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:45:17,899 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:45:17,907 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:45:17,907 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:45:17,907 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:45:17,908 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:45:17,908 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 01:45:17,908 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 01:45:17,909 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 227 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-30 01:45:17,919] [main] java.version = 21 [testng] 01:45:17,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:45:17,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:17,970 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-30_01-45-17.log] [testng] 01:45:17,972 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-05-30 01:45:17,974] [main] testng.directory = /data [testng] [2024-05-30 01:45:17,975] [main] testng.configDirectory = /config [testng] [2024-05-30 01:45:17,985] [main] testng.multiplier = 1.0 [testng] [2024-05-30 01:45:17,986] [main] testng.in-memory = false [testng] [2024-05-30 01:45:17,986] [main] testng.allow-missing = false [testng] [2024-05-30 01:45:17,986] [main] user.language = en [testng] [2024-05-30 01:45:17,986] [main] user.country = ${user.country} [testng] [2024-05-30 01:45:17,987] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-05-30 01:45:19,751] [main] ---------------------------------------- [testng] [2024-05-30 01:45:19,751] [main] Total files: 46 [testng] [2024-05-30 01:45:19,751] [main] Scan time: 1.764 s (38 ms/file) [testng] [2024-05-30 01:45:19,752] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-30 01:45:37,426] [pool-1-thread-1] Initializing /data/christian/080807epi/080807epi2.vws: [testng] 01:45:37,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:45:37,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:37,429 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-30_01-45-37.log] [testng] 01:45:37,429 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ce145ff - End of configuration. [testng] [2024-05-30 01:45:37,509] [pool-1-thread-12] Initializing /data/samples/fibre.vws: [testng] 01:45:37,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:45:37,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:37,511 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-30_01-45-37.log] [testng] 01:45:37,511 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76714228 - End of configuration. [testng] [2024-05-30 01:45:37,534] [pool-1-thread-11] Initializing /data/andreas/090812E4.vws: [testng] 01:45:37,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:45:37,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:37,536 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-30_01-45-37.log] [testng] 01:45:37,536 |-INFO in ch.qos.logback.core.sift.SiftProcessor@548af19e - End of configuration. [testng] [2024-05-30 01:45:38,472] [pool-1-thread-10] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] 01:45:38,473 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:45:38,473 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:38,473 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-30_01-45-38.log] [testng] 01:45:38,474 |-INFO in ch.qos.logback.core.sift.SiftProcessor@776d92f3 - End of configuration. [testng] [2024-05-30 01:45:40,051] [pool-1-thread-9] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] 01:45:40,052 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:45:40,052 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:40,053 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-30_01-45-40.log] [testng] 01:45:40,054 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9849fab - End of configuration. [testng] [2024-05-30 01:45:40,120] [pool-1-thread-8] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws: [testng] 01:45:40,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:45:40,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:40,122 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-30_01-45-40.log] [testng] 01:45:40,122 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5786e395 - End of configuration. [testng] [2024-05-30 01:45:40,192] [pool-1-thread-7] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] 01:45:40,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:45:40,193 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:40,194 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-30_01-45-40.log] [testng] 01:45:40,194 |-INFO in ch.qos.logback.core.sift.SiftProcessor@330a35a6 - End of configuration. [testng] [2024-05-30 01:45:40,435] [pool-1-thread-6] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] 01:45:40,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:45:40,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:40,436 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-30_01-45-40.log] [testng] 01:45:40,437 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d25c260 - End of configuration. [testng] [2024-05-30 01:45:40,467] [pool-1-thread-5] Initializing /data/stephan/two sequences.vws: [testng] 01:45:40,467 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:45:40,467 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:40,468 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-30_01-45-40.log] [testng] 01:45:40,468 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40c419c8 - End of configuration. [testng] [2024-05-30 01:45:40,485] [pool-1-thread-4] Initializing /data/imagesc-84715/working.vws: [testng] 01:45:40,485 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:45:40,485 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:40,486 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-30_01-45-40.log] [testng] 01:45:40,487 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49b5f0d6 - End of configuration. [testng] [2024-05-30 01:45:40,932] [pool-1-thread-3] Initializing /data/andreas/090811E1.vws: [testng] 01:45:40,933 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:45:40,933 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:40,933 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-30_01-45-40.log] [testng] 01:45:40,934 |-INFO in ch.qos.logback.core.sift.SiftProcessor@376902e6 - End of configuration. [testng] [2024-05-30 01:45:43,582] [pool-1-thread-2] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] 01:45:43,582 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:45:43,582 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:43,583 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-30_01-45-43.log] [testng] 01:45:43,583 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53fe7d6 - End of configuration. [testng] [2024-05-30 01:45:48,782] [pool-1-thread-12] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] [2024-05-30 01:45:48,803] [pool-1-thread-6] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] [2024-05-30 01:45:48,851] [pool-1-thread-9] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] [2024-05-30 01:45:49,185] [pool-1-thread-5] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] [2024-05-30 01:45:49,450] [pool-1-thread-1] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws: [testng] [2024-05-30 01:45:49,489] [pool-1-thread-6] Initializing /data/imagesc-84715/not working.vws: [testng] [2024-05-30 01:45:49,665] [pool-1-thread-8] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] [2024-05-30 01:45:49,780] [pool-1-thread-9] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws: [testng] [2024-05-30 01:45:51,020] [pool-1-thread-12] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] [2024-05-30 01:45:55,489] [pool-1-thread-5] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] [2024-05-30 01:45:55,978] [pool-1-thread-7] Initializing /data/gerhard/test.vws: [testng] [2024-05-30 01:45:56,528] [pool-1-thread-5] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] [2024-05-30 01:45:56,675] [pool-1-thread-1] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.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 33 seconds Finished: SUCCESS