Started by upstream project "BIOFORMATS-test-repo" build number 314 originally caused by: Started by upstream project "Trigger" build number 336 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins18051155956588706953.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_49782_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 test-automated: [testng] File leak detector installed [testng] 02:35:12,226 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:35:12,227 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 02:35:12,227 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:35:12,229 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:35:12,229 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:35:12,229 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:35:12,229 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:35:12,229 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:35:12,230 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:35:12,230 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:35:12,230 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:35:12,230 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:35:12,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:35:12,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:35:12,474 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:35:12,474 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:35:12,482 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:35:12,482 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:35:12,482 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:35:12,482 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:35:12,482 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 02:35:12,483 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 02:35:12,483 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 253 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-10 02:35:12,493] [main] java.version = 1.8.0_342 [testng] 02:35:12,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:35:12,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:12,540 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-10_02-35-12.log] [testng] 02:35:12,542 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2025-01-10 02:35:12,544] [main] testng.directory = /data [testng] [2025-01-10 02:35:12,544] [main] testng.configDirectory = /config [testng] [2025-01-10 02:35:12,556] [main] testng.multiplier = 1.0 [testng] [2025-01-10 02:35:12,557] [main] testng.in-memory = false [testng] [2025-01-10 02:35:12,557] [main] testng.allow-missing = false [testng] [2025-01-10 02:35:12,557] [main] user.language = en [testng] [2025-01-10 02:35:12,557] [main] user.country = ${user.country} [testng] [2025-01-10 02:35:12,557] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2025-01-10 02:35:19,764] [main] ---------------------------------------- [testng] [2025-01-10 02:35:19,764] [main] Total files: 46 [testng] [2025-01-10 02:35:19,765] [main] Scan time: 7.207 s (156 ms/file) [testng] [2025-01-10 02:35:19,765] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-10 02:35:49,522] [pool-1-thread-1] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] 02:35:49,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:35:49,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:49,524 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-10_02-35-49.log] [testng] 02:35:49,524 |-INFO in ch.qos.logback.core.sift.SiftProcessor@123d774a - End of configuration. [testng] [2025-01-10 02:35:50,115] [pool-1-thread-12] Initializing /data/andreas/090812E4.vws: [testng] 02:35:50,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:35:50,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:50,116 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-10_02-35-50.log] [testng] 02:35:50,117 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ee205ec - End of configuration. [testng] [2025-01-10 02:35:51,553] [pool-1-thread-11] Initializing /data/stephan/two sequences.vws: [testng] 02:35:51,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:35:51,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:51,554 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-10_02-35-51.log] [testng] 02:35:51,555 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19e57f7b - End of configuration. [testng] [2025-01-10 02:35:51,780] [pool-1-thread-10] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] 02:35:51,780 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:35:51,781 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:51,781 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-10_02-35-51.log] [testng] 02:35:51,782 |-INFO in ch.qos.logback.core.sift.SiftProcessor@584a296d - End of configuration. [testng] [2025-01-10 02:35:52,214] [pool-1-thread-9] Initializing /data/imagesc-84715/working.vws: [testng] 02:35:52,214 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:35:52,214 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:52,215 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-10_02-35-52.log] [testng] 02:35:52,215 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47260f61 - End of configuration. [testng] [2025-01-10 02:35:52,831] [pool-1-thread-8] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws: [testng] 02:35:52,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:35:52,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:52,831 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-10_02-35-52.log] [testng] 02:35:52,832 |-INFO in ch.qos.logback.core.sift.SiftProcessor@424cf364 - End of configuration. [testng] [2025-01-10 02:35:53,103] [pool-1-thread-7] Initializing /data/imagesc-84715/not working.vws: [testng] 02:35:53,103 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:35:53,103 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:53,104 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-10_02-35-53.log] [testng] 02:35:53,104 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e9c9bfd - End of configuration. [testng] [2025-01-10 02:35:53,456] [pool-1-thread-6] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] 02:35:53,456 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:35:53,456 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:53,457 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-10_02-35-53.log] [testng] 02:35:53,457 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1fac60c5 - End of configuration. [testng] [2025-01-10 02:35:53,784] [pool-1-thread-5] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] 02:35:53,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:35:53,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:53,785 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-10_02-35-53.log] [testng] 02:35:53,786 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73caaf25 - End of configuration. [testng] [2025-01-10 02:35:54,046] [pool-1-thread-4] Initializing /data/gerhard/test.vws: [testng] 02:35:54,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:35:54,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:54,047 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-10_02-35-54.log] [testng] 02:35:54,047 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62316aee - End of configuration. [testng] [2025-01-10 02:35:54,393] [pool-1-thread-3] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] 02:35:54,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:35:54,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:54,394 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-10_02-35-54.log] [testng] 02:35:54,394 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d42c481 - End of configuration. [testng] [2025-01-10 02:35:54,594] [pool-1-thread-2] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws: [testng] 02:35:54,594 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:35:54,594 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:54,595 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-10_02-35-54.log] [testng] 02:35:54,595 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14e9b76c - End of configuration. [testng] [2025-01-10 02:36:00,031] [pool-1-thread-4] Initializing /data/christian/080807epi/080807epi2.vws: [testng] [2025-01-10 02:36:00,490] [pool-1-thread-1] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] [2025-01-10 02:36:06,293] [pool-1-thread-1] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] [2025-01-10 02:36:10,475] [pool-1-thread-5] Initializing /data/samples/fibre.vws: [testng] [2025-01-10 02:36:13,268] [pool-1-thread-7] Initializing /data/andreas/090811E1.vws: [testng] [2025-01-10 02:36:18,146] [pool-1-thread-5] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] [2025-01-10 02:36:20,755] [pool-1-thread-3] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] [2025-01-10 02:36:21,560] [pool-1-thread-4] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws: [testng] [2025-01-10 02:36:22,609] [pool-1-thread-10] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] [2025-01-10 02:36:26,553] [pool-1-thread-8] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] [2025-01-10 02:36:27,293] [pool-1-thread-6] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] [2025-01-10 02:36:27,578] [pool-1-thread-11] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] [2025-01-10 02:36:27,845] [pool-1-thread-9] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1325, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 13 minutes 20 seconds Finished: SUCCESS