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Started by upstream project "BIOFORMATS-test-repo" build number 268 originally caused by: Started by upstream project "Trigger" build number 291 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins9336969671604073403.sh + '[' leica-tcs = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_42411_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] 12:25:43,273 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 12:25:43,274 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 12:25:43,274 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:25:43,275 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:25:43,276 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 12:25:43,276 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 12:25:43,277 |-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] 12:25:43,277 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:25:43,277 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:25:43,278 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 12:25:43,278 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 12:25:43,278 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 12:25:43,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 12:25:43,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 12:25:43,470 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 12:25:43,470 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 12:25:43,475 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 12:25:43,475 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 12:25:43,475 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 12:25:43,476 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 12:25:43,476 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 12:25:43,477 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 12:25:43,477 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 200 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-26 12:25:43,485] [main] java.version = 11.0.16 [testng] 12:25:43,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 12:25:43,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:25:43,530 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-26_12-25-43.log] [testng] 12:25:43,532 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-11-26 12:25:43,533] [main] testng.directory = /data [testng] [2024-11-26 12:25:43,534] [main] testng.configDirectory = /config [testng] [2024-11-26 12:25:43,543] [main] testng.multiplier = 1.0 [testng] [2024-11-26 12:25:43,544] [main] testng.in-memory = false [testng] [2024-11-26 12:25:43,544] [main] testng.allow-missing = false [testng] [2024-11-26 12:25:43,544] [main] user.language = en [testng] [2024-11-26 12:25:43,544] [main] user.country = ${user.country} [testng] [2024-11-26 12:25:43,544] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-26 12:26:01,167] [main] ---------------------------------------- [testng] [2024-11-26 12:26:01,167] [main] Total files: 944 [testng] [2024-11-26 12:26:01,167] [main] Scan time: 17.622 s (18 ms/file) [testng] [2024-11-26 12:26:01,167] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-26 12:28:08,282] [pool-1-thread-1] Initializing /data/stjude/AntoDayzerocy3OVP.tif: [testng] 12:28:08,282 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 12:28:08,283 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:28:08,284 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-26_12-28-08.log] [testng] 12:28:08,284 |-INFO in ch.qos.logback.core.sift.SiftProcessor@203d5c89 - End of configuration. [testng] [2024-11-26 12:28:10,513] [pool-1-thread-12] Initializing /data/stjude/AntoDay1cy3/c01f0001.TIF: [testng] 12:28:10,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 12:28:10,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:28:10,514 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-26_12-28-10.log] [testng] 12:28:10,514 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d3ace31 - End of configuration. [testng] [2024-11-26 12:28:12,244] [pool-1-thread-11] Initializing /data/stjude/AntoDay4dblmy2GRP.tif: [testng] 12:28:12,245 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 12:28:12,245 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:28:12,245 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-26_12-28-12.log] [testng] 12:28:12,246 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24740e7c - End of configuration. [testng] [2024-11-26 12:28:14,376] [pool-1-thread-10] Initializing /data/stjude/AntoDayzerocy3GRP.tif: [testng] 12:28:14,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 12:28:14,376 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:28:14,377 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-26_12-28-14.log] [testng] 12:28:14,377 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28ad673 - End of configuration. [testng] [2024-11-26 12:28:16,545] [pool-1-thread-9] Initializing /data/primate/Leica_Image.tif: [testng] 12:28:16,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 12:28:16,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:28:16,546 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-26_12-28-16.log] [testng] 12:28:16,546 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1cb7e286 - End of configuration. [testng] [2024-11-26 12:28:18,312] [pool-1-thread-8] Initializing /data/stjude/Antoday1dblcatsglGRP.tif: [testng] 12:28:18,312 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 12:28:18,312 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:28:18,312 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-26_12-28-18.log] [testng] 12:28:18,313 |-INFO in ch.qos.logback.core.sift.SiftProcessor@533c8502 - End of configuration. [testng] [2024-11-26 12:28:20,131] [pool-1-thread-7] Initializing /data/stjude/Antoday1dblcat2dataGRP.tif: [testng] 12:28:20,131 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 12:28:20,131 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:28:20,132 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-26_12-28-20.log] [testng] 12:28:20,132 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b9cd275 - End of configuration. [testng] [2024-11-26 12:28:22,081] [pool-1-thread-6] Initializing /data/brian/Series002_z01.tif: [testng] 12:28:22,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 12:28:22,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:28:22,082 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-26_12-28-22.log] [testng] 12:28:22,082 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a31e4f3 - End of configuration. [testng] [2024-11-26 12:28:25,013] [pool-1-thread-5] Initializing /data/martin/Series028_z00_ch00.tif: [testng] 12:28:25,013 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 12:28:25,013 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:28:25,013 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-26_12-28-25.log] [testng] 12:28:25,014 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d9d036b - End of configuration. [testng] [2024-11-26 12:28:27,703] [pool-1-thread-4] Initializing /data/stjude/AntoDay1dblGRP.tif: [testng] 12:28:27,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 12:28:27,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:28:27,704 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-26_12-28-27.log] [testng] 12:28:27,705 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e0b8c09 - End of configuration. [testng] [2024-11-26 12:28:29,686] [pool-1-thread-3] Initializing /data/dave/series 35/042911_Series035_t00_z000_ch00.tif: [testng] 12:28:29,686 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 12:28:29,686 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:28:29,687 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-26_12-28-29.log] [testng] 12:28:29,687 |-INFO in ch.qos.logback.core.sift.SiftProcessor@403871ce - End of configuration. [testng] [2024-11-26 12:29:43,777] [pool-1-thread-2] Initializing /data/brian/Series002_z00_ch00.tif: [testng] 12:29:43,777 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 12:29:43,777 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:29:43,778 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-26_12-29-43.log] [testng] 12:29:43,778 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2cae361 - End of configuration. [testng] [2024-11-26 12:29:58,463] [pool-1-thread-12] Initializing /data/stjude/AntoDay4dblcatdataGRP.tif: [testng] [2024-11-26 12:30:01,055] [pool-1-thread-9] Initializing /data/stjude/AntoDay4dblmyGRP.tif: [testng] [2024-11-26 12:30:05,244] [pool-1-thread-6] Initializing /data/stjude/Antoday1dblmysglGRP.tif: [testng] 14:10:58,896 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 14:10:58,896 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:10:58,897 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-26_14-10-58.log] [testng] 14:10:58,897 |-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: 105 minutes 20 seconds Finished: SUCCESS