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Started by upstream project "BIOFORMATS-test-repo" build number 109 originally caused by: Started by upstream project "Trigger" build number 122 originally caused by: Started by user devspace 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/jenkins13301786401824619931.sh + '[' leica-tcs = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_17008_merge_ci -v /uod/idr/repos/curated/leica-tcs:/data -v /uod/idr-scratch/merge-ci/curated/leica-tcs:/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] 13:15:19,066 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 13:15:19,068 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 13:15:19,068 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 13:15:19,069 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 13:15:19,070 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 13:15:19,070 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 13:15:19,071 |-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] 13:15:19,071 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 13:15:19,071 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 13:15:19,072 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 13:15:19,072 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 13:15:19,072 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 13:15:19,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 13:15:19,272 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 13:15:19,297 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 13:15:19,297 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 13:15:19,304 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 13:15:19,304 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 13:15:19,304 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 13:15:19,304 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 13:15:19,304 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 13:15:19,305 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 13:15:19,305 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 234 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-02 13:15:19,316] [main] java.version = 11.0.16 [testng] 13:15:19,320 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 13:15:19,320 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:15:19,371 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-02_13-15-19.log] [testng] 13:15:19,373 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-07-02 13:15:19,376] [main] testng.directory = /data [testng] [2024-07-02 13:15:19,377] [main] testng.configDirectory = /config [testng] [2024-07-02 13:15:19,392] [main] testng.multiplier = 1.0 [testng] [2024-07-02 13:15:19,393] [main] testng.in-memory = false [testng] [2024-07-02 13:15:19,393] [main] testng.allow-missing = false [testng] [2024-07-02 13:15:19,394] [main] user.language = en [testng] [2024-07-02 13:15:19,394] [main] user.country = ${user.country} [testng] [2024-07-02 13:15:19,394] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-02 13:15:29,606] [main] ---------------------------------------- [testng] [2024-07-02 13:15:29,606] [main] Total files: 944 [testng] [2024-07-02 13:15:29,607] [main] Scan time: 10.212 s (10 ms/file) [testng] [2024-07-02 13:15:29,607] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-02 13:16:00,728] [pool-1-thread-1] Initializing /data/stjude/AntoDay1cy3/c01f0001.TIF: [testng] 13:16:00,728 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 13:16:00,729 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:16:00,730 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-02_13-16-00.log] [testng] 13:16:00,731 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32098ac9 - End of configuration. [testng] [2024-07-02 13:16:00,760] [pool-1-thread-12] Initializing /data/stjude/AntoDay4dblmy2GRP.tif: [testng] 13:16:00,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 13:16:00,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:16:00,762 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-02_13-16-00.log] [testng] 13:16:00,763 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5fd89b00 - End of configuration. [testng] [2024-07-02 13:16:00,811] [pool-1-thread-11] Initializing /data/primate/Leica_Image.tif: [testng] 13:16:00,812 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 13:16:00,812 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:16:00,813 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-02_13-16-00.log] [testng] 13:16:00,813 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57b36ea0 - End of configuration. [testng] [2024-07-02 13:16:00,888] [pool-1-thread-10] Initializing /data/stjude/AntoDay1dblGRP.tif: [testng] 13:16:00,888 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 13:16:00,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:16:00,889 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-02_13-16-00.log] [testng] 13:16:00,890 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ad99595 - End of configuration. [testng] [2024-07-02 13:16:00,928] [pool-1-thread-9] Initializing /data/brian/Series002_z01.tif: [testng] 13:16:00,928 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 13:16:00,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:16:00,929 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-02_13-16-00.log] [testng] 13:16:00,930 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f3a56b - End of configuration. [testng] [2024-07-02 13:16:00,978] [pool-1-thread-8] Initializing /data/dave/series 35/042911_Series035_t00_z000_ch00.tif: [testng] 13:16:00,979 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 13:16:00,979 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:16:00,979 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-02_13-16-00.log] [testng] 13:16:00,980 |-INFO in ch.qos.logback.core.sift.SiftProcessor@362cfee2 - End of configuration. [testng] [2024-07-02 13:16:05,906] [pool-1-thread-7] Initializing /data/stjude/Antoday1dblcatsglGRP.tif: [testng] 13:16:05,906 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 13:16:05,906 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:16:05,907 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-02_13-16-05.log] [testng] 13:16:05,907 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9dcb50a - End of configuration. [testng] [2024-07-02 13:16:05,959] [pool-1-thread-6] Initializing /data/martin/Series028_z00_ch00.tif: [testng] 13:16:05,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 13:16:05,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:16:05,960 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-02_13-16-05.log] [testng] 13:16:05,960 |-INFO in ch.qos.logback.core.sift.SiftProcessor@453a23fe - End of configuration. [testng] [2024-07-02 13:16:05,991] [pool-1-thread-5] Initializing /data/stjude/Antoday1dblmysglGRP.tif: [testng] 13:16:05,991 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 13:16:05,991 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:16:05,992 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-02_13-16-05.log] [testng] 13:16:05,992 |-INFO in ch.qos.logback.core.sift.SiftProcessor@238a7fa3 - End of configuration. [testng] [2024-07-02 13:16:06,030] [pool-1-thread-4] Initializing /data/brian/Series002_z00_ch00.tif: [testng] 13:16:06,030 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 13:16:06,030 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:16:06,031 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-02_13-16-06.log] [testng] 13:16:06,031 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b51095e - End of configuration. [testng] [2024-07-02 13:16:06,062] [pool-1-thread-3] Initializing /data/stjude/AntoDayzerocy3GRP.tif: [testng] 13:16:06,062 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 13:16:06,062 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:16:06,063 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-02_13-16-06.log] [testng] 13:16:06,064 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dd62a96 - End of configuration. [testng] [2024-07-02 13:16:06,090] [pool-1-thread-2] Initializing /data/stjude/AntoDay4dblcatdataGRP.tif: [testng] 13:16:06,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 13:16:06,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:16:06,090 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-02_13-16-06.log] [testng] 13:16:06,091 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2750c33 - End of configuration. [testng] [2024-07-02 13:16:08,639] [pool-1-thread-4] Initializing /data/stjude/AntoDay4dblmyGRP.tif: [testng] [2024-07-02 13:16:08,675] [pool-1-thread-11] Initializing /data/stjude/Antoday1dblcat2dataGRP.tif: [testng] [2024-07-02 13:16:08,715] [pool-1-thread-2] Initializing /data/stjude/AntoDayzerocy3OVP.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 795, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 9 minutes 49 seconds Finished: SUCCESS