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Started by upstream project "BIOFORMATS-test-repo" build number 242 originally caused by: Started by upstream project "Trigger" build number 267 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/jenkins1521068339648904289.sh + '[' leica-scn = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_38129_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 [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] 03:07:28,824 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:07:28,825 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 03:07:28,825 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:07:28,826 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:07:28,827 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:07:28,827 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:07:28,827 |-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] 03:07:28,827 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:07:28,828 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:07:28,829 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:07:28,829 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:07:28,829 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:07:29,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:07:29,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:07:29,024 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:07:29,024 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:07:29,029 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:07:29,029 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:07:29,029 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:07:29,030 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:07:29,030 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 03:07:29,031 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 03:07:29,031 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 203 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-02 03:07:29,039] [main] java.version = 11.0.16 [testng] 03:07:29,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:07:29,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:07:29,083 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-02_03-07-29.log] [testng] 03:07:29,085 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-11-02 03:07:29,087] [main] testng.directory = /data [testng] [2024-11-02 03:07:29,087] [main] testng.configDirectory = /config [testng] [2024-11-02 03:07:29,096] [main] testng.multiplier = 1.0 [testng] [2024-11-02 03:07:29,097] [main] testng.in-memory = false [testng] [2024-11-02 03:07:29,098] [main] testng.allow-missing = false [testng] [2024-11-02 03:07:29,098] [main] user.language = en [testng] [2024-11-02 03:07:29,098] [main] user.country = ${user.country} [testng] [2024-11-02 03:07:29,098] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-02 03:07:53,989] [main] ---------------------------------------- [testng] [2024-11-02 03:07:53,989] [main] Total files: 12 [testng] [2024-11-02 03:07:53,989] [main] Scan time: 24.891 s (2074 ms/file) [testng] [2024-11-02 03:07:53,989] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 12 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-02 03:08:13,303] [pool-1-thread-1] Initializing /data/public/openslide/Leica-1/Leica-1.scn: [testng] 03:08:13,304 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:08:13,304 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:08:13,306 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-02_03-08-13.log] [testng] 03:08:13,306 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ea6926c - End of configuration. [testng] [2024-11-02 03:08:15,213] [pool-1-thread-12] Initializing /data/michael/collection_0000008286_2012-05-23 17_20_46 opened usig LOCI.tif: [testng] 03:08:15,213 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:08:15,213 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:08:15,214 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-02_03-08-15.log] [testng] 03:08:15,214 |-INFO in ch.qos.logback.core.sift.SiftProcessor@329d22c3 - End of configuration. [testng] [2024-11-02 03:08:17,135] [pool-1-thread-11] Initializing /data/public/openslide/Leica-2/Leica-2.scn: [testng] 03:08:17,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:08:17,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:08:17,136 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-02_03-08-17.log] [testng] 03:08:17,137 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e805a3 - End of configuration. [testng] [2024-11-02 03:08:19,196] [pool-1-thread-10] Initializing /data/michael/collection_0000008286_2012-05-23 17_20_46 fullresolution.jpg: [testng] 03:08:19,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:08:19,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:08:19,197 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-02_03-08-19.log] [testng] 03:08:19,198 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5eefcd3d - End of configuration. [testng] [2024-11-02 03:08:19,403] [pool-1-thread-9] Initializing /data/scott/Oral_Biology_13 (1).scn: [testng] 03:08:19,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:08:19,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:08:19,404 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-02_03-08-19.log] [testng] 03:08:19,405 |-INFO in ch.qos.logback.core.sift.SiftProcessor@568c8ef5 - End of configuration. [testng] [2024-11-02 03:08:21,397] [pool-1-thread-8] Initializing /data/public/openslide/Leica-3/Leica-3.scn: [testng] 03:08:21,398 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:08:21,398 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:08:21,398 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-02_03-08-21.log] [testng] 03:08:21,399 |-INFO in ch.qos.logback.core.sift.SiftProcessor@530eb4ff - End of configuration. [testng] [2024-11-02 03:08:23,102] [pool-1-thread-7] Initializing /data/mihaela/UCLAD_0000000280_2011-02-10 13_32_55Z.scn: [testng] 03:08:23,102 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:08:23,102 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:08:23,103 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-02_03-08-23.log] [testng] 03:08:23,103 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29658e9f - End of configuration. [testng] [2024-11-02 03:08:24,790] [pool-1-thread-6] Initializing /data/michael/collection_0000008286_2012-05-23 17_20_46.scn: [testng] 03:08:24,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:08:24,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:08:24,791 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-02_03-08-24.log] [testng] 03:08:24,792 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f7a0fd6 - End of configuration. [testng] [2024-11-02 03:08:26,394] [pool-1-thread-5] Initializing /data/scott/ImageCollection_0000000418_2010-10-27 13_31_31Z.scn: [testng] 03:08:26,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:08:26,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:08:26,395 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-02_03-08-26.log] [testng] 03:08:26,395 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ef3fcc7 - End of configuration. [testng] [2024-11-02 03:08:28,076] [pool-1-thread-4] Initializing /data/qa-17671/132223-12_022a1963-b32e-467f-8242-b51a5295951f.SCN: [testng] 03:08:28,076 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:08:28,076 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:08:28,077 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-02_03-08-28.log] [testng] 03:08:28,077 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f323388 - End of configuration. [testng] [2024-11-02 03:08:29,726] [pool-1-thread-3] Initializing /data/qa-11049/HP15.4994_2015-04-28.scn: [testng] 03:08:29,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:08:29,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:08:29,728 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-02_03-08-29.log] [testng] 03:08:29,728 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51a1729e - End of configuration. [testng] [2024-11-02 03:08:31,116] [pool-1-thread-2] Initializing /data/qa-10469/Slide_907790L_DAPI_Ki67.scn: [testng] 03:08:31,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:08:31,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:08:31,117 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-02_03-08-31.log] [testng] 03:08:31,117 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50d6777f - 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: 2 minutes 31 seconds Finished: SUCCESS