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Started by upstream project "BIOFORMATS-test-repo" build number 106 originally caused by: Started by upstream project "Trigger" build number 118 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/jenkins10357908694638936233.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_16447_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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 01:47:51,924 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:47:51,926 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 01:47:51,926 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:47:51,927 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:47:51,927 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:47:51,928 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:47:51,928 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:47:51,928 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:47:51,929 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:47:51,930 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:47:51,930 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:47:51,930 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:47:52,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:47:52,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:47:52,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:47:52,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:47:52,168 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:47:52,168 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:47:52,168 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:47:52,169 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:47:52,169 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 01:47:52,170 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 01:47:52,170 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 241 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-29 01:47:52,182] [main] java.version = 11.0.16 [testng] 01:47:52,189 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:47:52,189 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:47:52,239 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-29_01-47-52.log] [testng] 01:47:52,242 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-06-29 01:47:52,245] [main] testng.directory = /data [testng] [2024-06-29 01:47:52,246] [main] testng.configDirectory = /config [testng] [2024-06-29 01:47:52,259] [main] testng.multiplier = 1.0 [testng] [2024-06-29 01:47:52,261] [main] testng.in-memory = false [testng] [2024-06-29 01:47:52,261] [main] testng.allow-missing = false [testng] [2024-06-29 01:47:52,261] [main] user.language = en [testng] [2024-06-29 01:47:52,261] [main] user.country = ${user.country} [testng] [2024-06-29 01:47:52,261] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-29 01:47:53,956] [main] ---------------------------------------- [testng] [2024-06-29 01:47:53,956] [main] Total files: 46 [testng] [2024-06-29 01:47:53,956] [main] Scan time: 1.695 s (36 ms/file) [testng] [2024-06-29 01:47:53,956] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-29 01:48:09,838] [pool-1-thread-1] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] 01:48:09,838 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:48:09,838 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:09,840 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-29_01-48-09.log] [testng] 01:48:09,841 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e7c473c - End of configuration. [testng] [2024-06-29 01:48:09,959] [pool-1-thread-12] Initializing /data/imagesc-84715/not working.vws: [testng] 01:48:09,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:48:09,960 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:09,962 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-29_01-48-09.log] [testng] 01:48:09,962 |-INFO in ch.qos.logback.core.sift.SiftProcessor@310bc2d5 - End of configuration. [testng] [2024-06-29 01:48:10,137] [pool-1-thread-11] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws: [testng] 01:48:10,137 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:48:10,137 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:10,138 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-29_01-48-10.log] [testng] 01:48:10,138 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bb7b6c5 - End of configuration. [testng] [2024-06-29 01:48:10,182] [pool-1-thread-10] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] 01:48:10,183 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:48:10,183 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:10,183 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-29_01-48-10.log] [testng] 01:48:10,184 |-INFO in ch.qos.logback.core.sift.SiftProcessor@548af19e - End of configuration. [testng] [2024-06-29 01:48:10,261] [pool-1-thread-9] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] 01:48:10,261 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:48:10,261 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:10,262 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-29_01-48-10.log] [testng] 01:48:10,263 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56b5710c - End of configuration. [testng] [2024-06-29 01:48:10,280] [pool-1-thread-8] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] 01:48:10,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:48:10,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:10,281 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-29_01-48-10.log] [testng] 01:48:10,281 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a88d2bc - End of configuration. [testng] [2024-06-29 01:48:10,364] [pool-1-thread-7] Initializing /data/gerhard/test.vws: [testng] 01:48:10,365 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:48:10,365 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:10,365 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-29_01-48-10.log] [testng] 01:48:10,366 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4945dc7d - End of configuration. [testng] [2024-06-29 01:48:10,540] [pool-1-thread-6] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws: [testng] 01:48:10,541 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:48:10,541 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:10,542 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-29_01-48-10.log] [testng] 01:48:10,543 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44d0ac9e - End of configuration. [testng] [2024-06-29 01:48:11,080] [pool-1-thread-5] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] 01:48:11,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:48:11,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:11,081 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-29_01-48-11.log] [testng] 01:48:11,082 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63eee6d - End of configuration. [testng] [2024-06-29 01:48:13,978] [pool-1-thread-4] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] 01:48:13,978 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:48:13,978 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:13,979 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-29_01-48-13.log] [testng] 01:48:13,979 |-INFO in ch.qos.logback.core.sift.SiftProcessor@376902e6 - End of configuration. [testng] [2024-06-29 01:48:13,994] [pool-1-thread-3] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] 01:48:13,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:48:13,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:13,995 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-29_01-48-13.log] [testng] 01:48:13,996 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53fe7d6 - End of configuration. [testng] [2024-06-29 01:48:14,028] [pool-1-thread-2] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] 01:48:14,028 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:48:14,028 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:14,029 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-29_01-48-14.log] [testng] 01:48:14,029 |-INFO in ch.qos.logback.core.sift.SiftProcessor@323d77ff - End of configuration. [testng] [2024-06-29 01:48:16,541] [pool-1-thread-3] Initializing /data/samples/fibre.vws: [testng] [2024-06-29 01:48:16,557] [pool-1-thread-2] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] [2024-06-29 01:48:16,744] [pool-1-thread-8] Initializing /data/andreas/090811E1.vws: [testng] [2024-06-29 01:48:18,889] [pool-1-thread-9] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] [2024-06-29 01:48:18,910] [pool-1-thread-4] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] [2024-06-29 01:48:18,924] [pool-1-thread-11] Initializing /data/stephan/two sequences.vws: [testng] [2024-06-29 01:48:19,158] [pool-1-thread-10] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] [2024-06-29 01:48:22,078] [pool-1-thread-3] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws: [testng] [2024-06-29 01:48:22,177] [pool-1-thread-9] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] [2024-06-29 01:48:23,412] [pool-1-thread-7] Initializing /data/christian/080807epi/080807epi2.vws: [testng] [2024-06-29 01:48:23,863] [pool-1-thread-1] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws: [testng] [2024-06-29 01:48:24,464] [pool-1-thread-12] Initializing /data/imagesc-84715/working.vws: [testng] [2024-06-29 01:48:25,018] [pool-1-thread-11] Initializing /data/andreas/090812E4.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 2 seconds Finished: SUCCESS