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Started by upstream project "BIOFORMATS-test-repo" build number 250 originally caused by: Started by upstream project "Trigger" build number 274 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/jenkins7658097437005906581.sh + '[' leica-tcs = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_39459_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] 05:08:31,891 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 05:08:31,892 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 05:08:31,892 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:08:31,893 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:08:31,894 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 05:08:31,894 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 05:08:31,895 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 05:08:31,895 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:08:31,895 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:08:31,896 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 05:08:31,896 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 05:08:31,896 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 05:08:32,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 05:08:32,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 05:08:32,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 05:08:32,082 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 05:08:32,087 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 05:08:32,087 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 05:08:32,087 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 05:08:32,088 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 05:08:32,088 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 05:08:32,089 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 05:08:32,089 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 194 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-09 05:08:32,097] [main] java.version = 11.0.16 [testng] 05:08:32,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:08:32,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:32,141 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-09_05-08-32.log] [testng] 05:08:32,142 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-11-09 05:08:32,144] [main] testng.directory = /data [testng] [2024-11-09 05:08:32,144] [main] testng.configDirectory = /config [testng] [2024-11-09 05:08:32,154] [main] testng.multiplier = 1.0 [testng] [2024-11-09 05:08:32,155] [main] testng.in-memory = false [testng] [2024-11-09 05:08:32,155] [main] testng.allow-missing = false [testng] [2024-11-09 05:08:32,155] [main] user.language = en [testng] [2024-11-09 05:08:32,155] [main] user.country = ${user.country} [testng] [2024-11-09 05:08:32,155] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-09 05:09:10,231] [main] ---------------------------------------- [testng] [2024-11-09 05:09:10,231] [main] Total files: 944 [testng] [2024-11-09 05:09:10,231] [main] Scan time: 38.075 s (40 ms/file) [testng] [2024-11-09 05:09:10,231] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-09 05:11:21,224] [pool-1-thread-1] Initializing /data/primate/Leica_Image.tif: [testng] 05:11:21,224 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 05:11:21,225 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:11:21,226 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-09_05-11-21.log] [testng] 05:11:21,227 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f42d80e - End of configuration. [testng] [2024-11-09 05:11:23,092] [pool-1-thread-12] Initializing /data/brian/Series002_z00_ch00.tif: [testng] 05:11:23,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 05:11:23,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:11:23,093 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-09_05-11-23.log] [testng] 05:11:23,093 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46d075f4 - End of configuration. [testng] [2024-11-09 05:11:25,026] [pool-1-thread-11] Initializing /data/dave/series 35/042911_Series035_t00_z000_ch00.tif: [testng] 05:11:25,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 05:11:25,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:11:25,027 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-09_05-11-25.log] [testng] 05:11:25,027 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6477d1f3 - End of configuration. [testng] [2024-11-09 05:12:46,057] [pool-1-thread-10] Initializing /data/martin/Series028_z00_ch00.tif: [testng] 05:12:46,058 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 05:12:46,058 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:12:46,058 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-09_05-12-46.log] [testng] 05:12:46,059 |-INFO in ch.qos.logback.core.sift.SiftProcessor@661b4b59 - End of configuration. [testng] [2024-11-09 05:12:48,999] [pool-1-thread-9] Initializing /data/stjude/AntoDayzerocy3GRP.tif: [testng] 05:12:49,000 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 05:12:49,000 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:12:49,000 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-09_05-12-49.log] [testng] 05:12:49,000 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4352a7fc - End of configuration. [testng] [2024-11-09 05:12:51,504] [pool-1-thread-8] Initializing /data/stjude/AntoDay4dblmyGRP.tif: [testng] 05:12:51,504 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 05:12:51,504 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:12:51,505 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-09_05-12-51.log] [testng] 05:12:51,505 |-INFO in ch.qos.logback.core.sift.SiftProcessor@537c3ed7 - End of configuration. [testng] [2024-11-09 05:12:53,630] [pool-1-thread-7] Initializing /data/stjude/Antoday1dblcatsglGRP.tif: [testng] 05:12:53,630 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 05:12:53,630 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:12:53,631 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-09_05-12-53.log] [testng] 05:12:53,631 |-INFO in ch.qos.logback.core.sift.SiftProcessor@613cff18 - End of configuration. [testng] [2024-11-09 05:12:55,725] [pool-1-thread-6] Initializing /data/stjude/Antoday1dblmysglGRP.tif: [testng] 05:12:55,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 05:12:55,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:12:55,725 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-09_05-12-55.log] [testng] 05:12:55,726 |-INFO in ch.qos.logback.core.sift.SiftProcessor@217af219 - End of configuration. [testng] [2024-11-09 05:12:57,798] [pool-1-thread-5] Initializing /data/stjude/Antoday1dblcat2dataGRP.tif: [testng] 05:12:57,798 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 05:12:57,798 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:12:57,798 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-09_05-12-57.log] [testng] 05:12:57,799 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c6546f3 - End of configuration. [testng] [2024-11-09 05:12:59,894] [pool-1-thread-4] Initializing /data/stjude/AntoDayzerocy3OVP.tif: [testng] 05:12:59,895 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 05:12:59,895 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:12:59,895 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-09_05-12-59.log] [testng] 05:12:59,895 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55318f3d - End of configuration. [testng] [2024-11-09 05:13:02,227] [pool-1-thread-3] Initializing /data/stjude/AntoDay1cy3/c01f0001.TIF: [testng] 05:13:02,227 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 05:13:02,227 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:13:02,228 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-09_05-13-02.log] [testng] 05:13:02,228 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d2a3847 - End of configuration. [testng] [2024-11-09 05:13:04,237] [pool-1-thread-2] Initializing /data/stjude/AntoDay1dblGRP.tif: [testng] 05:13:04,237 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 05:13:04,237 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:13:04,238 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-09_05-13-04.log] [testng] 05:13:04,238 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68b54c21 - End of configuration. [testng] [2024-11-09 05:13:20,576] [pool-1-thread-3] Initializing /data/brian/Series002_z01.tif: [testng] [2024-11-09 05:13:23,999] [pool-1-thread-1] Initializing /data/stjude/AntoDay4dblmy2GRP.tif: [testng] [2024-11-09 05:13:29,850] [pool-1-thread-7] Initializing /data/stjude/AntoDay4dblcatdataGRP.tif: [testng] 07:13:09,216 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 07:13:09,216 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:13:09,217 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-09_07-13-09.log] [testng] 07:13:09,218 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36d33f4 - 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: 124 minutes 42 seconds Finished: SUCCESS