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Started by upstream project "BIOFORMATS-test-repo" build number 18 originally caused by: Started by upstream project "Trigger" build number 21 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins18149448512263527557.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_2178_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] 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] 00:45:10,029 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:45:10,031 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 00:45:10,031 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:45:10,033 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:45:10,034 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:45:10,034 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:45:10,034 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:45:10,034 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:45:10,035 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:45:10,036 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:45:10,037 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:45:10,037 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:45:10,265 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:45:10,265 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:45:10,289 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:45:10,289 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:45:10,295 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:45:10,295 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:45:10,295 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:45:10,296 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:45:10,296 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 00:45:10,296 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 00:45:10,297 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 262 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-31 00:45:10,306] [main] java.version = 17.0.2 [testng] 00:45:10,310 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:45:10,310 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:10,352 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-31_00-45-10.log] [testng] 00:45:10,353 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-03-31 00:45:10,355] [main] testng.directory = /data [testng] [2024-03-31 00:45:10,356] [main] testng.configDirectory = /config [testng] [2024-03-31 00:45:10,365] [main] testng.multiplier = 1.0 [testng] [2024-03-31 00:45:10,366] [main] testng.in-memory = false [testng] [2024-03-31 00:45:10,366] [main] testng.allow-missing = false [testng] [2024-03-31 00:45:10,366] [main] user.language = en [testng] [2024-03-31 00:45:10,366] [main] user.country = ${user.country} [testng] [2024-03-31 00:45:10,366] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-31 00:45:12,190] [main] ---------------------------------------- [testng] [2024-03-31 00:45:12,191] [main] Total files: 46 [testng] [2024-03-31 00:45:12,191] [main] Scan time: 1.824 s (39 ms/file) [testng] [2024-03-31 00:45:12,192] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-31 00:45:29,240] [pool-1-thread-1] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] 00:45:29,240 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:45:29,240 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:29,241 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-31_00-45-29.log] [testng] 00:45:29,242 |-INFO in ch.qos.logback.core.sift.SiftProcessor@493e75a0 - End of configuration. [testng] [2024-03-31 00:45:29,344] [pool-1-thread-12] Initializing /data/andreas/090812E4.vws: [testng] 00:45:29,344 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:45:29,344 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:29,345 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-31_00-45-29.log] [testng] 00:45:29,345 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d70a299 - End of configuration. [testng] [2024-03-31 00:45:30,361] [pool-1-thread-11] Initializing /data/imagesc-84715/working.vws: [testng] 00:45:30,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:45:30,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:30,362 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-31_00-45-30.log] [testng] 00:45:30,363 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78792ff0 - End of configuration. [testng] [2024-03-31 00:45:30,836] [pool-1-thread-10] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] 00:45:30,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:45:30,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:30,837 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-31_00-45-30.log] [testng] 00:45:30,838 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7055fa48 - End of configuration. [testng] [2024-03-31 00:45:31,043] [pool-1-thread-9] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] 00:45:31,043 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:45:31,043 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:31,044 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-31_00-45-31.log] [testng] 00:45:31,045 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69a167a3 - End of configuration. [testng] [2024-03-31 00:45:31,060] [pool-1-thread-8] Initializing /data/andreas/090811E1.vws: [testng] 00:45:31,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:45:31,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:31,061 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-31_00-45-31.log] [testng] 00:45:31,062 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7667eb9e - End of configuration. [testng] [2024-03-31 00:45:33,780] [pool-1-thread-7] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] 00:45:33,781 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:45:33,781 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:33,782 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-31_00-45-33.log] [testng] 00:45:33,783 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2eccac63 - End of configuration. [testng] [2024-03-31 00:45:33,800] [pool-1-thread-6] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] 00:45:33,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:45:33,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:33,801 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-31_00-45-33.log] [testng] 00:45:33,802 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c0015ab - End of configuration. [testng] [2024-03-31 00:45:35,402] [pool-1-thread-5] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] 00:45:35,402 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:45:35,402 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:35,404 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-31_00-45-35.log] [testng] 00:45:35,404 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3aace575 - End of configuration. [testng] [2024-03-31 00:45:38,693] [pool-1-thread-4] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws: [testng] 00:45:38,693 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:45:38,693 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:38,694 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-31_00-45-38.log] [testng] 00:45:38,694 |-INFO in ch.qos.logback.core.sift.SiftProcessor@178a1e09 - End of configuration. [testng] [2024-03-31 00:45:39,357] [pool-1-thread-3] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] 00:45:39,357 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:45:39,358 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:39,359 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-31_00-45-39.log] [testng] 00:45:39,359 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a6daf5c - End of configuration. [testng] [2024-03-31 00:45:39,375] [pool-1-thread-2] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] 00:45:39,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:45:39,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:45:39,376 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-31_00-45-39.log] [testng] 00:45:39,377 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1dfa18 - End of configuration. [testng] [2024-03-31 00:45:45,581] [pool-1-thread-3] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] [2024-03-31 00:45:45,616] [pool-1-thread-7] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] [2024-03-31 00:45:45,650] [pool-1-thread-9] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] [2024-03-31 00:45:45,684] [pool-1-thread-1] Initializing /data/imagesc-84715/not working.vws: [testng] [2024-03-31 00:45:46,407] [pool-1-thread-7] Initializing /data/samples/fibre.vws: [testng] [2024-03-31 00:45:46,432] [pool-1-thread-9] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws: [testng] [2024-03-31 00:45:46,493] [pool-1-thread-3] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] [2024-03-31 00:45:46,956] [pool-1-thread-7] Initializing /data/christian/080807epi/080807epi2.vws: [testng] [2024-03-31 00:45:48,042] [pool-1-thread-10] Initializing /data/gerhard/test.vws: [testng] [2024-03-31 00:45:48,514] [pool-1-thread-7] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] [2024-03-31 00:45:49,102] [pool-1-thread-7] Initializing /data/stephan/two sequences.vws: [testng] [2024-03-31 00:45:49,456] [pool-1-thread-10] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws: [testng] [2024-03-31 00:45:50,126] [pool-1-thread-9] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.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 27 seconds Finished: SUCCESS