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Started by upstream project "BIOFORMATS-test-repo" build number 2 originally caused by: Started by upstream project "Trigger" build number 3 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins12185603575897781785.sh + '[' leica-scn = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_259_merge_ci -v /uod/idr/repos/curated/leica-scn:/data -v /uod/idr-scratch/merge-ci/curated/leica-scn:/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] 01:40:31,222 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:40:31,223 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 01:40:31,223 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:40:31,225 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:40:31,225 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:40:31,225 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:40:31,225 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:40:31,225 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:40:31,226 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:40:31,226 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:40:31,226 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:40:31,226 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:40:31,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:40:31,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:40:31,500 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:40:31,500 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:40:31,508 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:40:31,508 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:40:31,508 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:40:31,509 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:40:31,509 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 01:40:31,510 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 01:40:31,510 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 284 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-15 01:40:31,520] [main] java.version = 1.8.0_342 [testng] 01:40:31,524 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:40:31,524 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:31,570 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-15_01-40-31.log] [testng] 01:40:31,572 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-03-15 01:40:31,574] [main] testng.directory = /data [testng] [2024-03-15 01:40:31,574] [main] testng.configDirectory = /config [testng] [2024-03-15 01:40:31,588] [main] testng.multiplier = 1.0 [testng] [2024-03-15 01:40:31,589] [main] testng.in-memory = false [testng] [2024-03-15 01:40:31,589] [main] testng.allow-missing = false [testng] [2024-03-15 01:40:31,589] [main] user.language = en [testng] [2024-03-15 01:40:31,589] [main] user.country = ${user.country} [testng] [2024-03-15 01:40:31,589] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-03-15 01:40:49,180] [main] ---------------------------------------- [testng] [2024-03-15 01:40:49,180] [main] Total files: 12 [testng] [2024-03-15 01:40:49,180] [main] Scan time: 17.591 s (1465 ms/file) [testng] [2024-03-15 01:40:49,181] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 12 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-15 01:40:52,849] [pool-1-thread-1] Initializing /data/scott/Oral_Biology_13 (1).scn: [testng] 01:40:52,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:40:52,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:52,850 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-15_01-40-52.log] [testng] 01:40:52,850 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a60ad2d - End of configuration. [testng] [2024-03-15 01:40:53,240] [pool-1-thread-12] Initializing /data/scott/ImageCollection_0000000418_2010-10-27 13_31_31Z.scn: [testng] 01:40:53,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:40:53,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:53,242 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-15_01-40-53.log] [testng] 01:40:53,242 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2cdda362 - End of configuration. [testng] [2024-03-15 01:40:53,506] [pool-1-thread-11] Initializing /data/michael/collection_0000008286_2012-05-23 17_20_46 opened usig LOCI.tif: [testng] 01:40:53,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:40:53,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:53,507 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-15_01-40-53.log] [testng] 01:40:53,508 |-INFO in ch.qos.logback.core.sift.SiftProcessor@de31b2f - End of configuration. [testng] [2024-03-15 01:40:53,782] [pool-1-thread-10] Initializing /data/public/openslide/Leica-3/Leica-3.scn: [testng] 01:40:53,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:40:53,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:53,783 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-15_01-40-53.log] [testng] 01:40:53,820 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60b24da4 - End of configuration. [testng] [2024-03-15 01:40:54,196] [pool-1-thread-9] Initializing /data/michael/collection_0000008286_2012-05-23 17_20_46.scn: [testng] 01:40:54,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:40:54,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:54,198 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-15_01-40-54.log] [testng] 01:40:54,199 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1aabeb25 - End of configuration. [testng] [2024-03-15 01:40:54,544] [pool-1-thread-8] Initializing /data/qa-17671/132223-12_022a1963-b32e-467f-8242-b51a5295951f.SCN: [testng] 01:40:54,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:40:54,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:54,545 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-15_01-40-54.log] [testng] 01:40:54,546 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b7dce56 - End of configuration. [testng] [2024-03-15 01:40:54,820] [pool-1-thread-7] Initializing /data/mihaela/UCLAD_0000000280_2011-02-10 13_32_55Z.scn: [testng] 01:40:54,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:40:54,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:54,821 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-15_01-40-54.log] [testng] 01:40:54,822 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40adfedd - End of configuration. [testng] [2024-03-15 01:40:55,291] [pool-1-thread-6] Initializing /data/qa-11049/HP15.4994_2015-04-28.scn: [testng] 01:40:55,291 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:40:55,291 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:55,292 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-15_01-40-55.log] [testng] 01:40:55,293 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d408e51 - End of configuration. [testng] [2024-03-15 01:40:55,576] [pool-1-thread-5] Initializing /data/public/openslide/Leica-2/Leica-2.scn: [testng] 01:40:55,577 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:40:55,577 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:55,578 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-15_01-40-55.log] [testng] 01:40:55,578 |-INFO in ch.qos.logback.core.sift.SiftProcessor@337de29 - End of configuration. [testng] [2024-03-15 01:40:55,894] [pool-1-thread-4] Initializing /data/qa-10469/Slide_907790L_DAPI_Ki67.scn: [testng] 01:40:55,895 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:40:55,895 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:55,895 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-15_01-40-55.log] [testng] 01:40:55,896 |-INFO in ch.qos.logback.core.sift.SiftProcessor@404131bc - End of configuration. [testng] [2024-03-15 01:40:56,266] [pool-1-thread-3] Initializing /data/michael/collection_0000008286_2012-05-23 17_20_46 fullresolution.jpg: [testng] 01:40:56,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:40:56,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:56,267 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-15_01-40-56.log] [testng] 01:40:56,268 |-INFO in ch.qos.logback.core.sift.SiftProcessor@165dfca9 - End of configuration. [testng] [2024-03-15 01:40:56,362] [pool-1-thread-2] Initializing /data/public/openslide/Leica-1/Leica-1.scn: [testng] 01:40:56,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:40:56,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:56,363 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-15_01-40-56.log] [testng] 01:40:56,364 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b1a94b3 - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 636, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 1 minute 34 seconds Finished: SUCCESS