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Started by upstream project "BIOFORMATS-test-repo" build number 234 originally caused by: Started by upstream project "Trigger" build number 259 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/jenkins2702353207622805579.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_36766_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] 02:31:27,328 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:31:27,330 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 02:31:27,330 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:31:27,331 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:31:27,331 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:31:27,331 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:31:27,331 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:31:27,331 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:31:27,332 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:31:27,332 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:31:27,332 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:31:27,332 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:31:27,552 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:31:27,552 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:31:27,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:31:27,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:31:27,589 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:31:27,589 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:31:27,590 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:31:27,590 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:31:27,590 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 02:31:27,591 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 02:31:27,591 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 259 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-25 02:31:27,601] [main] java.version = 1.8.0_342 [testng] 02:31:27,604 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:31:27,604 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:31:27,648 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-25_02-31-27.log] [testng] 02:31:27,650 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-10-25 02:31:27,652] [main] testng.directory = /data [testng] [2024-10-25 02:31:27,652] [main] testng.configDirectory = /config [testng] [2024-10-25 02:31:27,663] [main] testng.multiplier = 1.0 [testng] [2024-10-25 02:31:27,664] [main] testng.in-memory = false [testng] [2024-10-25 02:31:27,664] [main] testng.allow-missing = false [testng] [2024-10-25 02:31:27,664] [main] user.language = en [testng] [2024-10-25 02:31:27,664] [main] user.country = ${user.country} [testng] [2024-10-25 02:31:27,664] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-25 02:31:38,361] [main] ---------------------------------------- [testng] [2024-10-25 02:31:38,361] [main] Total files: 46 [testng] [2024-10-25 02:31:38,361] [main] Scan time: 10.697 s (232 ms/file) [testng] [2024-10-25 02:31:38,361] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-25 02:32:10,937] [pool-1-thread-1] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] 02:32:10,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:32:10,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:10,938 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-25_02-32-10.log] [testng] 02:32:10,938 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57f3be38 - End of configuration. [testng] [2024-10-25 02:32:11,856] [pool-1-thread-12] Initializing /data/gerhard/test.vws: [testng] 02:32:11,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:32:11,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:11,858 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-25_02-32-11.log] [testng] 02:32:11,858 |-INFO in ch.qos.logback.core.sift.SiftProcessor@688946f8 - End of configuration. [testng] [2024-10-25 02:32:12,202] [pool-1-thread-11] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] 02:32:12,203 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:32:12,203 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:12,203 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-25_02-32-12.log] [testng] 02:32:12,204 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55329d8b - End of configuration. [testng] [2024-10-25 02:32:13,039] [pool-1-thread-10] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] 02:32:13,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:32:13,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:13,040 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-25_02-32-13.log] [testng] 02:32:13,040 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7587a381 - End of configuration. [testng] [2024-10-25 02:32:14,823] [pool-1-thread-9] Initializing /data/samples/fibre.vws: [testng] 02:32:14,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:32:14,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:14,824 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-25_02-32-14.log] [testng] 02:32:14,825 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7085249c - End of configuration. [testng] [2024-10-25 02:32:15,009] [pool-1-thread-8] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws: [testng] 02:32:15,010 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:32:15,010 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:15,010 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-25_02-32-15.log] [testng] 02:32:15,010 |-INFO in ch.qos.logback.core.sift.SiftProcessor@477d57b4 - End of configuration. [testng] [2024-10-25 02:32:15,858] [pool-1-thread-7] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] 02:32:15,858 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:32:15,858 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:15,859 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-25_02-32-15.log] [testng] 02:32:15,859 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9356c34 - End of configuration. [testng] [2024-10-25 02:32:16,390] [pool-1-thread-6] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] 02:32:16,390 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:32:16,390 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:16,391 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-25_02-32-16.log] [testng] 02:32:16,391 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49e26837 - End of configuration. [testng] [2024-10-25 02:32:16,738] [pool-1-thread-5] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] 02:32:16,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:32:16,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:16,739 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-25_02-32-16.log] [testng] 02:32:16,739 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f56c671 - End of configuration. [testng] [2024-10-25 02:32:20,975] [pool-1-thread-4] Initializing /data/andreas/090812E4.vws: [testng] 02:32:20,976 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:32:20,976 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:20,977 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-25_02-32-20.log] [testng] 02:32:20,977 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ca30366 - End of configuration. [testng] [2024-10-25 02:32:22,729] [pool-1-thread-3] Initializing /data/imagesc-84715/not working.vws: [testng] 02:32:22,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:32:22,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:22,730 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-25_02-32-22.log] [testng] 02:32:22,731 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76faa2c6 - End of configuration. [testng] [2024-10-25 02:32:23,067] [pool-1-thread-2] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] 02:32:23,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:32:23,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:32:23,068 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-25_02-32-23.log] [testng] 02:32:23,069 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b513f3d - End of configuration. [testng] [2024-10-25 02:32:28,868] [pool-1-thread-9] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] [2024-10-25 02:32:33,210] [pool-1-thread-12] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] [2024-10-25 02:32:33,915] [pool-1-thread-11] Initializing /data/imagesc-84715/working.vws: [testng] [2024-10-25 02:32:34,797] [pool-1-thread-1] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] [2024-10-25 02:32:35,602] [pool-1-thread-2] Initializing /data/andreas/090811E1.vws: [testng] [2024-10-25 02:32:46,310] [pool-1-thread-6] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] [2024-10-25 02:32:47,509] [pool-1-thread-3] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] [2024-10-25 02:32:49,541] [pool-1-thread-7] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws: [testng] [2024-10-25 02:32:52,417] [pool-1-thread-3] Initializing /data/stephan/two sequences.vws: [testng] [2024-10-25 02:32:54,730] [pool-1-thread-1] Initializing /data/christian/080807epi/080807epi2.vws: [testng] [2024-10-25 02:32:56,133] [pool-1-thread-6] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] [2024-10-25 02:32:56,485] [pool-1-thread-12] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws: [testng] [2024-10-25 02:32:57,388] [pool-1-thread-8] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.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 28 seconds Finished: SUCCESS