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Started by upstream project "BIOFORMATS-test-repo" build number 260 originally caused by: Started by upstream project "Trigger" build number 284 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins2937893994567743180.sh + '[' leica-tcs = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_41099_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] 03:37:54,908 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:37:54,910 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 03:37:54,910 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:37:54,911 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:37:54,911 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:37:54,912 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:37:54,912 |-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] 03:37:54,912 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:37:54,912 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:37:54,913 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:37:54,913 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:37:54,914 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:37:55,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:37:55,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:37:55,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:37:55,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:37:55,106 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:37:55,106 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:37:55,106 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:37:55,107 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:37:55,107 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 03:37:55,107 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 03:37:55,107 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 195 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-19 03:37:55,115] [main] java.version = 11.0.16 [testng] 03:37:55,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:37:55,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:37:55,160 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-19_03-37-55.log] [testng] 03:37:55,162 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-11-19 03:37:55,164] [main] testng.directory = /data [testng] [2024-11-19 03:37:55,164] [main] testng.configDirectory = /config [testng] [2024-11-19 03:37:55,173] [main] testng.multiplier = 1.0 [testng] [2024-11-19 03:37:55,174] [main] testng.in-memory = false [testng] [2024-11-19 03:37:55,174] [main] testng.allow-missing = false [testng] [2024-11-19 03:37:55,175] [main] user.language = en [testng] [2024-11-19 03:37:55,175] [main] user.country = ${user.country} [testng] [2024-11-19 03:37:55,175] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-19 03:38:09,855] [main] ---------------------------------------- [testng] [2024-11-19 03:38:09,855] [main] Total files: 944 [testng] [2024-11-19 03:38:09,855] [main] Scan time: 14.68 s (15 ms/file) [testng] [2024-11-19 03:38:09,855] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-19 03:39:49,589] [pool-1-thread-1] Initializing /data/stjude/AntoDayzerocy3OVP.tif: [testng] 03:39:49,589 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:39:49,589 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:39:49,591 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-19_03-39-49.log] [testng] 03:39:49,591 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48aac0ac - End of configuration. [testng] [2024-11-19 03:39:51,201] [pool-1-thread-12] Initializing /data/stjude/AntoDay1cy3/c01f0001.TIF: [testng] 03:39:51,201 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:39:51,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:39:51,203 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-19_03-39-51.log] [testng] 03:39:51,203 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f8655e1 - End of configuration. [testng] [2024-11-19 03:39:52,519] [pool-1-thread-11] Initializing /data/stjude/AntoDay4dblmy2GRP.tif: [testng] 03:39:52,519 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:39:52,519 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:39:52,519 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-19_03-39-52.log] [testng] 03:39:52,520 |-INFO in ch.qos.logback.core.sift.SiftProcessor@596a8d2a - End of configuration. [testng] [2024-11-19 03:39:54,109] [pool-1-thread-10] Initializing /data/stjude/AntoDayzerocy3GRP.tif: [testng] 03:39:54,109 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:39:54,109 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:39:54,110 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-19_03-39-54.log] [testng] 03:39:54,110 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f784cd3 - End of configuration. [testng] [2024-11-19 03:39:55,692] [pool-1-thread-9] Initializing /data/primate/Leica_Image.tif: [testng] 03:39:55,692 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:39:55,692 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:39:55,693 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-19_03-39-55.log] [testng] 03:39:55,693 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d910a18 - End of configuration. [testng] [2024-11-19 03:39:57,042] [pool-1-thread-8] Initializing /data/stjude/Antoday1dblcatsglGRP.tif: [testng] 03:39:57,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:39:57,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:39:57,043 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-19_03-39-57.log] [testng] 03:39:57,043 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1237da59 - End of configuration. [testng] [2024-11-19 03:39:58,470] [pool-1-thread-7] Initializing /data/stjude/Antoday1dblcat2dataGRP.tif: [testng] 03:39:58,470 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:39:58,470 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:39:58,471 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-19_03-39-58.log] [testng] 03:39:58,471 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15b25e5c - End of configuration. [testng] [2024-11-19 03:39:59,924] [pool-1-thread-6] Initializing /data/brian/Series002_z01.tif: [testng] 03:39:59,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:39:59,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:39:59,925 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-19_03-39-59.log] [testng] 03:39:59,925 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dbf6937 - End of configuration. [testng] [2024-11-19 03:40:02,297] [pool-1-thread-5] Initializing /data/martin/Series028_z00_ch00.tif: [testng] 03:40:02,298 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:40:02,298 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:02,298 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-19_03-40-02.log] [testng] 03:40:02,299 |-INFO in ch.qos.logback.core.sift.SiftProcessor@809be87 - End of configuration. [testng] [2024-11-19 03:40:04,491] [pool-1-thread-4] Initializing /data/stjude/AntoDay1dblGRP.tif: [testng] 03:40:04,492 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:40:04,492 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:04,492 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-19_03-40-04.log] [testng] 03:40:04,493 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2888f6d5 - End of configuration. [testng] [2024-11-19 03:40:06,075] [pool-1-thread-3] Initializing /data/dave/series 35/042911_Series035_t00_z000_ch00.tif: [testng] 03:40:06,076 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:40:06,076 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:06,076 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-19_03-40-06.log] [testng] 03:40:06,076 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d366103 - End of configuration. [testng] [2024-11-19 03:40:59,680] [pool-1-thread-2] Initializing /data/brian/Series002_z00_ch00.tif: [testng] 03:40:59,680 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:40:59,681 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:40:59,681 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-19_03-40-59.log] [testng] 03:40:59,705 |-INFO in ch.qos.logback.core.sift.SiftProcessor@216ecb53 - End of configuration. [testng] [2024-11-19 03:41:10,102] [pool-1-thread-12] Initializing /data/stjude/AntoDay4dblcatdataGRP.tif: [testng] [2024-11-19 03:41:11,928] [pool-1-thread-9] Initializing /data/stjude/AntoDay4dblmyGRP.tif: [testng] [2024-11-19 03:41:14,866] [pool-1-thread-6] Initializing /data/stjude/Antoday1dblmysglGRP.tif: [testng] 04:50:00,623 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:50:00,623 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:50:00,624 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-19_04-50-00.log] [testng] 04:50:00,625 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a17b2e3 - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 795, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 72 minutes 13 seconds Finished: SUCCESS