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Started by upstream project "BIOFORMATS-test-repo" build number 18 originally caused by: Started by upstream project "Trigger" build number 21 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/jenkins10605956813461010483.sh + '[' afi = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_2185_merge_ci -v /uod/idr/repos/curated/afi:/data -v /uod/idr-scratch/merge-ci/curated/afi:/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] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 00:50:41,776 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:50:41,778 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 00:50:41,778 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:50:41,779 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:50:41,780 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:50:41,781 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:50:41,781 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:50:41,781 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:50:41,782 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:50:41,783 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:50:41,784 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:50:41,784 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:50:42,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:50:42,069 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:50:42,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:50:42,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:50:42,127 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:50:42,128 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:50:42,128 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:50:42,129 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:50:42,129 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 00:50:42,131 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 00:50:42,131 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 349 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-31 00:50:42,151] [main] java.version = 17.0.2 [testng] 00:50:42,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:50:42,162 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:42,235 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-31_00-50-42.log] [testng] 00:50:42,237 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-03-31 00:50:42,240] [main] testng.directory = /data [testng] [2024-03-31 00:50:42,240] [main] testng.configDirectory = /config [testng] [2024-03-31 00:50:42,254] [main] testng.multiplier = 1.0 [testng] [2024-03-31 00:50:42,256] [main] testng.in-memory = false [testng] [2024-03-31 00:50:42,256] [main] testng.allow-missing = false [testng] [2024-03-31 00:50:42,256] [main] user.language = en [testng] [2024-03-31 00:50:42,256] [main] user.country = ${user.country} [testng] [2024-03-31 00:50:42,256] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-31 00:50:43,332] [main] ---------------------------------------- [testng] [2024-03-31 00:50:43,333] [main] Total files: 16 [testng] [2024-03-31 00:50:43,333] [main] Scan time: 1.076 s (67 ms/file) [testng] [2024-03-31 00:50:43,333] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-31 00:50:54,810] [pool-1-thread-1] Initializing /data/samples/5347.afi: [testng] 00:50:54,811 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:50:54,811 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:54,813 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-31_00-50-54.log] [testng] 00:50:54,813 |-INFO in ch.qos.logback.core.sift.SiftProcessor@bb9474d - End of configuration. [testng] [2024-03-31 00:50:54,941] [pool-1-thread-12] Initializing /data/samples/5414.afi: [testng] 00:50:54,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:50:54,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:54,944 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-31_00-50-54.log] [testng] 00:50:54,945 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ffc12ef - End of configuration. [testng] [2024-03-31 00:50:55,197] [pool-1-thread-11] Initializing /data/samples/5407.afi: [testng] 00:50:55,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:50:55,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:55,198 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-31_00-50-55.log] [testng] 00:50:55,199 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ba8b25b - End of configuration. [testng] [2024-03-31 00:50:55,275] [pool-1-thread-10] Initializing /data/samples/5351.afi: [testng] 00:50:55,275 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:50:55,276 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:55,277 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-31_00-50-55.log] [testng] 00:50:55,278 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ba2cebc - End of configuration. [testng] [2024-03-31 00:50:55,474] [pool-1-thread-9] Initializing /data/samples/5343.afi: [testng] 00:50:55,475 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:50:55,475 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:55,476 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-31_00-50-55.log] [testng] 00:50:55,476 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74b1f578 - End of configuration. [testng] [2024-03-31 00:50:55,630] [pool-1-thread-8] Initializing /data/samples/5383.afi: [testng] 00:50:55,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:50:55,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:55,632 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-31_00-50-55.log] [testng] 00:50:55,633 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15647d95 - End of configuration. [testng] [2024-03-31 00:50:55,757] [pool-1-thread-7] Initializing /data/samples/5440.afi: [testng] 00:50:55,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:50:55,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:55,758 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-31_00-50-55.log] [testng] 00:50:55,759 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f69c42c - End of configuration. [testng] [2024-03-31 00:50:55,972] [pool-1-thread-6] Initializing /data/samples/5358.afi: [testng] 00:50:55,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:50:55,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:55,975 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-31_00-50-55.log] [testng] 00:50:55,978 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3cfc718b - End of configuration. [testng] [2024-03-31 00:50:56,099] [pool-1-thread-5] Initializing /data/samples/5365.afi: [testng] 00:50:56,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:50:56,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:56,101 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-31_00-50-56.log] [testng] 00:50:56,101 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d958f26 - End of configuration. [testng] [2024-03-31 00:50:56,263] [pool-1-thread-4] Initializing /data/samples/5446.afi: [testng] 00:50:56,264 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:50:56,264 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:56,265 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-31_00-50-56.log] [testng] 00:50:56,266 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35a95803 - End of configuration. [testng] [2024-03-31 00:50:56,493] [pool-1-thread-3] Initializing /data/samples/5371.afi: [testng] 00:50:56,493 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:50:56,493 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:56,494 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-31_00-50-56.log] [testng] 00:50:56,495 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5db1f2c1 - End of configuration. [testng] [2024-03-31 00:50:56,771] [pool-1-thread-2] Initializing /data/samples/5387.afi: [testng] 00:50:56,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:50:56,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:56,775 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-31_00-50-56.log] [testng] 00:50:56,776 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d481e9f - End of configuration. [testng] [2024-03-31 00:51:55,838] [pool-1-thread-6] Initializing /data/samples/5306.afi: [testng] [2024-03-31 00:51:57,319] [pool-1-thread-4] Initializing /data/samples/5400.afi: [testng] [2024-03-31 00:51:59,875] [pool-1-thread-5] Initializing /data/samples/5339.afi: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 795, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 2 minutes 30 seconds Finished: SUCCESS