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Started by upstream project "BIOFORMATS-test-repo" build number 278 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins10491324962419063538.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_43853_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] 10:47:02,942 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 10:47:02,944 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 10:47:02,945 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:47:02,946 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:47:02,946 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 10:47:02,947 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 10:47:02,947 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 10:47:02,947 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:47:02,948 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:47:02,948 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 10:47:02,949 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 10:47:02,949 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 10:47:03,125 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 10:47:03,126 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 10:47:03,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 10:47:03,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 10:47:03,155 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 10:47:03,155 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 10:47:03,155 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 10:47:03,155 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 10:47:03,155 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 10:47:03,156 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 10:47:03,156 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 208 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-03 10:47:03,166] [main] java.version = 11.0.16 [testng] 10:47:03,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 10:47:03,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:47:03,213 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-03_10-47-03.log] [testng] 10:47:03,214 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-12-03 10:47:03,216] [main] testng.directory = /data [testng] [2024-12-03 10:47:03,217] [main] testng.configDirectory = /config [testng] [2024-12-03 10:47:03,226] [main] testng.multiplier = 1.0 [testng] [2024-12-03 10:47:03,228] [main] testng.in-memory = false [testng] [2024-12-03 10:47:03,228] [main] testng.allow-missing = false [testng] [2024-12-03 10:47:03,228] [main] user.language = en [testng] [2024-12-03 10:47:03,228] [main] user.country = ${user.country} [testng] [2024-12-03 10:47:03,228] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-03 10:47:25,567] [main] ---------------------------------------- [testng] [2024-12-03 10:47:25,567] [main] Total files: 46 [testng] [2024-12-03 10:47:25,567] [main] Scan time: 22.339 s (485 ms/file) [testng] [2024-12-03 10:47:25,567] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-03 10:48:47,155] [pool-1-thread-1] Initializing /data/imagesc-84715/working.vws: [testng] 10:48:47,155 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 10:48:47,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:48:47,157 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-03_10-48-47.log] [testng] 10:48:47,158 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a28b473 - End of configuration. [testng] [2024-12-03 10:48:49,194] [pool-1-thread-12] Initializing /data/andreas/090812E4.vws: [testng] 10:48:49,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 10:48:49,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:48:49,196 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-03_10-48-49.log] [testng] 10:48:49,197 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d888d59 - End of configuration. [testng] [2024-12-03 10:48:52,909] [pool-1-thread-11] Initializing /data/andreas/090811E1.vws: [testng] 10:48:52,909 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 10:48:52,909 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:48:52,910 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-03_10-48-52.log] [testng] 10:48:52,910 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7445c664 - End of configuration. [testng] [2024-12-03 10:49:03,108] [pool-1-thread-10] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] 10:49:03,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 10:49:03,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:49:03,109 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-03_10-49-03.log] [testng] 10:49:03,110 |-INFO in ch.qos.logback.core.sift.SiftProcessor@128e4448 - End of configuration. [testng] [2024-12-03 10:49:04,701] [pool-1-thread-9] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] 10:49:04,701 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 10:49:04,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:49:04,702 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-03_10-49-04.log] [testng] 10:49:04,703 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62fc308d - End of configuration. [testng] [2024-12-03 10:49:06,316] [pool-1-thread-8] Initializing /data/samples/fibre.vws: [testng] 10:49:06,316 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 10:49:06,316 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:49:06,317 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-03_10-49-06.log] [testng] 10:49:06,317 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5df9bae7 - End of configuration. [testng] [2024-12-03 10:49:12,596] [pool-1-thread-7] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] 10:49:12,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 10:49:12,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:49:12,597 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-03_10-49-12.log] [testng] 10:49:12,597 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2db44267 - End of configuration. [testng] [2024-12-03 10:49:17,304] [pool-1-thread-6] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws: [testng] 10:49:17,304 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 10:49:17,304 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:49:17,305 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-03_10-49-17.log] [testng] 10:49:17,305 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11028e96 - End of configuration. [testng] [2024-12-03 10:49:19,204] [pool-1-thread-5] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] 10:49:19,205 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 10:49:19,205 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:49:19,205 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-03_10-49-19.log] [testng] 10:49:19,206 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3696316c - End of configuration. [testng] [2024-12-03 10:49:23,668] [pool-1-thread-4] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws: [testng] 10:49:23,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 10:49:23,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:49:23,669 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-03_10-49-23.log] [testng] 10:49:23,669 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f484c66 - End of configuration. [testng] [2024-12-03 10:49:25,885] [pool-1-thread-3] Initializing /data/imagesc-84715/not working.vws: [testng] 10:49:25,885 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 10:49:25,886 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:49:25,886 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-03_10-49-25.log] [testng] 10:49:25,886 |-INFO in ch.qos.logback.core.sift.SiftProcessor@446d70f0 - End of configuration. [testng] [2024-12-03 10:49:27,320] [pool-1-thread-2] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] 10:49:27,320 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 10:49:27,320 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:49:27,321 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-03_10-49-27.log] [testng] 10:49:27,321 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6924f8ee - End of configuration. [testng] [2024-12-03 10:49:48,668] [pool-1-thread-8] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] [2024-12-03 10:49:54,562] [pool-1-thread-5] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] [2024-12-03 10:50:17,125] [pool-1-thread-5] Initializing /data/gerhard/test.vws: [testng] [2024-12-03 10:50:25,351] [pool-1-thread-3] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws: [testng] [2024-12-03 10:50:30,307] [pool-1-thread-8] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] [2024-12-03 10:50:36,862] [pool-1-thread-5] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] [2024-12-03 10:50:43,841] [pool-1-thread-9] Initializing /data/stephan/two sequences.vws: [testng] [2024-12-03 10:50:45,596] [pool-1-thread-1] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] [2024-12-03 10:50:55,362] [pool-1-thread-8] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] [2024-12-03 10:51:08,196] [pool-1-thread-10] Initializing /data/christian/080807epi/080807epi2.vws: [testng] [2024-12-03 10:51:09,481] [pool-1-thread-1] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] [2024-12-03 10:51:38,316] [pool-1-thread-3] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws: [testng] [2024-12-03 10:51:39,606] [pool-1-thread-5] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1325, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 22 minutes 8 seconds Finished: SUCCESS