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Started by upstream project "BIOFORMATS-test-repo" build number 222 originally caused by: Started by upstream project "Trigger" build number 249 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/jenkins9382660141212238879.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35262_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] 07:10:40,610 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 07:10:40,611 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 07:10:40,611 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 07:10:40,612 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 07:10:40,613 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 07:10:40,613 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 07:10:40,613 |-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] 07:10:40,613 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 07:10:40,614 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 07:10:40,614 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 07:10:40,615 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 07:10:40,615 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 07:10:40,767 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 07:10:40,767 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 07:10:40,787 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 07:10:40,787 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 07:10:40,792 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 07:10:40,792 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 07:10:40,792 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 07:10:40,793 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 07:10:40,793 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 07:10:40,794 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 07:10:40,794 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 180 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-16 07:10:40,802] [main] java.version = 17.0.2 [testng] 07:10:40,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 07:10:40,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:10:40,842 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-16_07-10-40.log] [testng] 07:10:40,844 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-10-16 07:10:40,846] [main] testng.directory = /data [testng] [2024-10-16 07:10:40,846] [main] testng.configDirectory = /config [testng] [2024-10-16 07:10:40,854] [main] testng.multiplier = 1.0 [testng] [2024-10-16 07:10:40,855] [main] testng.in-memory = false [testng] [2024-10-16 07:10:40,855] [main] testng.allow-missing = false [testng] [2024-10-16 07:10:40,855] [main] user.language = en [testng] [2024-10-16 07:10:40,855] [main] user.country = ${user.country} [testng] [2024-10-16 07:10:40,855] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-16 07:12:55,307] [main] ---------------------------------------- [testng] [2024-10-16 07:12:55,307] [main] Total files: 46 [testng] [2024-10-16 07:12:55,307] [main] Scan time: 134.452 s (2922 ms/file) [testng] [2024-10-16 07:12:55,307] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-16 07:19:24,532] [pool-1-thread-1] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] 07:19:24,532 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 07:19:24,532 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:19:24,534 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-16_07-19-24.log] [testng] 07:19:24,534 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18cc83f4 - End of configuration. [testng] [2024-10-16 07:19:29,936] [pool-1-thread-12] Initializing /data/gerhard/test.vws: [testng] 07:19:29,936 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 07:19:29,936 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:19:29,937 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-16_07-19-29.log] [testng] 07:19:29,937 |-INFO in ch.qos.logback.core.sift.SiftProcessor@110f8673 - End of configuration. [testng] [2024-10-16 07:19:34,986] [pool-1-thread-11] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] 07:19:34,986 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 07:19:34,986 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:19:34,987 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-16_07-19-34.log] [testng] 07:19:34,987 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ee831c3 - End of configuration. [testng] [2024-10-16 07:19:51,591] [pool-1-thread-10] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] 07:19:51,591 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 07:19:51,591 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:19:51,592 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-16_07-19-51.log] [testng] 07:19:51,592 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64830adf - End of configuration. [testng] [2024-10-16 07:20:06,347] [pool-1-thread-9] Initializing /data/samples/fibre.vws: [testng] 07:20:06,348 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 07:20:06,348 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:20:06,349 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-16_07-20-06.log] [testng] 07:20:06,349 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d463720 - End of configuration. [testng] [2024-10-16 07:20:11,446] [pool-1-thread-8] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws: [testng] 07:20:11,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 07:20:11,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:20:11,447 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-16_07-20-11.log] [testng] 07:20:11,447 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66ebce75 - End of configuration. [testng] [2024-10-16 07:20:20,740] [pool-1-thread-7] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws: [testng] 07:20:20,740 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 07:20:20,740 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:20:20,741 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-16_07-20-20.log] [testng] 07:20:20,741 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21fc73f5 - End of configuration. [testng] [2024-10-16 07:20:26,919] [pool-1-thread-6] Initializing /data/christian/080807epi/080807epi2.vws: [testng] 07:20:26,920 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 07:20:26,920 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:20:26,920 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-16_07-20-26.log] [testng] 07:20:26,921 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4fb549d2 - End of configuration. [testng] [2024-10-16 07:20:32,226] [pool-1-thread-5] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] 07:20:32,227 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 07:20:32,227 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:20:32,227 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-16_07-20-32.log] [testng] 07:20:32,228 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2fd807ab - End of configuration. [testng] [2024-10-16 07:20:40,032] [pool-1-thread-4] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] 07:20:40,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 07:20:40,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:20:40,033 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-16_07-20-40.log] [testng] 07:20:40,033 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6195c8 - End of configuration. [testng] [2024-10-16 07:20:46,264] [pool-1-thread-3] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws: [testng] 07:20:46,264 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 07:20:46,264 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:20:46,265 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-16_07-20-46.log] [testng] 07:20:46,265 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58432731 - End of configuration. [testng] [2024-10-16 07:20:54,931] [pool-1-thread-2] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] 07:20:54,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 07:20:54,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:20:54,932 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-16_07-20-54.log] [testng] 07:20:54,932 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1cd14542 - End of configuration. [testng] [2024-10-16 07:22:08,772] [pool-1-thread-9] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws: [testng] [2024-10-16 07:22:16,342] [pool-1-thread-12] Initializing /data/imagesc-84715/not working.vws: [testng] [2024-10-16 07:22:37,642] [pool-1-thread-11] Initializing /data/andreas/090811E1.vws: [testng] [2024-10-16 07:24:45,043] [pool-1-thread-6] Initializing /data/imagesc-84715/working.vws: [testng] [2024-10-16 07:24:52,806] [pool-1-thread-4] Initializing /data/stephan/two sequences.vws: [testng] [2024-10-16 07:26:39,514] [pool-1-thread-12] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] [2024-10-16 07:26:55,629] [pool-1-thread-2] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] [2024-10-16 07:27:12,519] [pool-1-thread-7] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] [2024-10-16 07:27:30,003] [pool-1-thread-1] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] [2024-10-16 07:28:12,506] [pool-1-thread-9] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] [2024-10-16 07:28:40,435] [pool-1-thread-2] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] [2024-10-16 07:29:07,575] [pool-1-thread-7] Initializing /data/andreas/090812E4.vws: [testng] [2024-10-16 07:29:22,798] [pool-1-thread-5] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] 09:00:59,443 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 09:00:59,443 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:00:59,444 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-16_09-00-59.log] [testng] 09:00:59,445 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a2ddf26 - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1325, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 110 minutes 23 seconds Finished: SUCCESS