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Started by upstream project "BIOFORMATS-test-repo" build number 305 originally caused by: Started by upstream project "Trigger" build number 327 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins8919421083341473713.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_48297_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] 01:47:16,881 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:47:16,883 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 01:47:16,883 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:47:16,885 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:47:16,885 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:47:16,886 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:47:16,886 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:47:16,886 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:47:16,887 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:47:16,887 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:47:16,888 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:47:16,888 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:47:17,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:47:17,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:47:17,086 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:47:17,086 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:47:17,091 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:47:17,091 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:47:17,091 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:47:17,091 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:47:17,091 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 01:47:17,092 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 01:47:17,092 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 205 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-01 01:47:17,101] [main] java.version = 17.0.2 [testng] 01:47:17,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:47:17,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:47:17,151 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-01_01-47-17.log] [testng] 01:47:17,152 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2025-01-01 01:47:17,154] [main] testng.directory = /data [testng] [2025-01-01 01:47:17,154] [main] testng.configDirectory = /config [testng] [2025-01-01 01:47:17,162] [main] testng.multiplier = 1.0 [testng] [2025-01-01 01:47:17,163] [main] testng.in-memory = false [testng] [2025-01-01 01:47:17,163] [main] testng.allow-missing = false [testng] [2025-01-01 01:47:17,163] [main] user.language = en [testng] [2025-01-01 01:47:17,163] [main] user.country = ${user.country} [testng] [2025-01-01 01:47:17,163] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-01-01 01:47:30,069] [main] ---------------------------------------- [testng] [2025-01-01 01:47:30,070] [main] Total files: 46 [testng] [2025-01-01 01:47:30,070] [main] Scan time: 12.905 s (280 ms/file) [testng] [2025-01-01 01:47:30,070] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-01 01:48:15,780] [pool-1-thread-1] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] 01:48:15,780 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:48:15,780 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:15,782 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-01_01-48-15.log] [testng] 01:48:15,782 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68d7184 - End of configuration. [testng] [2025-01-01 01:48:16,229] [pool-1-thread-12] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] 01:48:16,229 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:48:16,229 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:16,230 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-01_01-48-16.log] [testng] 01:48:16,230 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78ad922f - End of configuration. [testng] [2025-01-01 01:48:16,836] [pool-1-thread-11] Initializing /data/stephan/two sequences.vws: [testng] 01:48:16,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:48:16,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:16,837 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-01_01-48-16.log] [testng] 01:48:16,838 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17c88852 - End of configuration. [testng] [2025-01-01 01:48:17,369] [pool-1-thread-10] Initializing /data/andreas/090811E1.vws: [testng] 01:48:17,370 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:48:17,370 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:17,370 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-01_01-48-17.log] [testng] 01:48:17,371 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42a50ad1 - End of configuration. [testng] [2025-01-01 01:48:22,808] [pool-1-thread-9] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws: [testng] 01:48:22,808 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:48:22,808 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:22,809 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-01_01-48-22.log] [testng] 01:48:22,809 |-INFO in ch.qos.logback.core.sift.SiftProcessor@506be020 - End of configuration. [testng] [2025-01-01 01:48:23,584] [pool-1-thread-8] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] 01:48:23,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:48:23,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:23,585 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-01_01-48-23.log] [testng] 01:48:23,586 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34cafbb9 - End of configuration. [testng] [2025-01-01 01:48:27,779] [pool-1-thread-7] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] 01:48:27,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:48:27,780 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:27,780 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-01_01-48-27.log] [testng] 01:48:27,781 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57da4f68 - End of configuration. [testng] [2025-01-01 01:48:28,346] [pool-1-thread-6] Initializing /data/gerhard/test.vws: [testng] 01:48:28,347 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:48:28,347 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:28,347 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-01_01-48-28.log] [testng] 01:48:28,348 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49bdaa01 - End of configuration. [testng] [2025-01-01 01:48:28,854] [pool-1-thread-5] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] 01:48:28,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:48:28,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:28,855 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-01_01-48-28.log] [testng] 01:48:28,855 |-INFO in ch.qos.logback.core.sift.SiftProcessor@705f4ee - End of configuration. [testng] [2025-01-01 01:48:30,488] [pool-1-thread-4] Initializing /data/imagesc-84715/working.vws: [testng] 01:48:30,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:48:30,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:30,489 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-01_01-48-30.log] [testng] 01:48:30,489 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a1377d0 - End of configuration. [testng] [2025-01-01 01:48:31,347] [pool-1-thread-3] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] 01:48:31,347 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:48:31,347 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:31,348 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-01_01-48-31.log] [testng] 01:48:31,348 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6599a867 - End of configuration. [testng] [2025-01-01 01:48:33,181] [pool-1-thread-2] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] 01:48:33,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:48:33,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:33,182 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-01_01-48-33.log] [testng] 01:48:33,182 |-INFO in ch.qos.logback.core.sift.SiftProcessor@158ecf1a - End of configuration. [testng] [2025-01-01 01:48:42,098] [pool-1-thread-6] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] [2025-01-01 01:48:44,292] [pool-1-thread-5] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws: [testng] [2025-01-01 01:48:45,518] [pool-1-thread-3] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] [2025-01-01 01:48:46,103] [pool-1-thread-2] Initializing /data/christian/080807epi/080807epi2.vws: [testng] [2025-01-01 01:49:04,159] [pool-1-thread-1] Initializing /data/imagesc-84715/not working.vws: [testng] [2025-01-01 01:49:04,850] [pool-1-thread-7] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws: [testng] [2025-01-01 01:49:05,502] [pool-1-thread-9] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] [2025-01-01 01:49:06,960] [pool-1-thread-2] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] [2025-01-01 01:49:07,834] [pool-1-thread-3] Initializing /data/andreas/090812E4.vws: [testng] [2025-01-01 01:49:09,779] [pool-1-thread-12] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] [2025-01-01 01:49:15,593] [pool-1-thread-11] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws: [testng] [2025-01-01 01:49:17,118] [pool-1-thread-4] Initializing /data/samples/fibre.vws: [testng] [2025-01-01 01:49:20,877] [pool-1-thread-9] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1325, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 15 minutes 17 seconds Finished: SUCCESS