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Started by upstream project "BIOFORMATS-test-repo" build number 101 originally caused by: Started by upstream project "Trigger" build number 112 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins16215660973741766868.sh + '[' imaris = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_15670_merge_ci -v /uod/idr/repos/curated/imaris:/data -v /uod/idr-scratch/merge-ci/curated/imaris:/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] 02:10:58,719 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:10:58,720 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 02:10:58,720 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:10:58,721 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:10:58,722 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:10:58,722 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:10:58,722 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:10:58,722 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:10:58,723 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:10:58,723 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:10:58,724 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:10:58,724 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:10:58,884 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:10:58,884 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:10:58,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:10:58,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:10:58,910 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:10:58,910 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:10:58,910 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:10:58,911 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:10:58,911 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 02:10:58,912 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 02:10:58,912 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 189 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-23 02:10:58,921] [main] java.version = 17.0.2 [testng] 02:10:58,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:10:58,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:58,972 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-23_02-10-58.log] [testng] 02:10:58,974 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-06-23 02:10:58,976] [main] testng.directory = /data [testng] [2024-06-23 02:10:58,976] [main] testng.configDirectory = /config [testng] [2024-06-23 02:10:58,985] [main] testng.multiplier = 1.0 [testng] [2024-06-23 02:10:58,985] [main] testng.in-memory = false [testng] [2024-06-23 02:10:58,985] [main] testng.allow-missing = false [testng] [2024-06-23 02:10:58,985] [main] user.language = en [testng] [2024-06-23 02:10:58,986] [main] user.country = ${user.country} [testng] [2024-06-23 02:10:58,986] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-23 02:11:05,797] [main] ---------------------------------------- [testng] [2024-06-23 02:11:05,797] [main] Total files: 67 [testng] [2024-06-23 02:11:05,797] [main] Scan time: 6.811 s (101 ms/file) [testng] [2024-06-23 02:11:05,797] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-23 02:11:28,960] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0010.ims: [testng] 02:11:28,960 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:11:28,960 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:28,961 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-23_02-11-28.log] [testng] 02:11:28,962 |-INFO in ch.qos.logback.core.sift.SiftProcessor@739d6656 - End of configuration. [testng] [2024-06-23 02:11:28,987] [pool-1-thread-12] Initializing /data/generated/10-31_E_t0004.ims: [testng] 02:11:28,987 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:11:28,987 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:28,988 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-23_02-11-28.log] [testng] 02:11:28,988 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12edb9f3 - End of configuration. [testng] [2024-06-23 02:11:29,007] [pool-1-thread-11] Initializing /data/qa-8019/wrong_num_dimensions.ims: [testng] 02:11:29,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:11:29,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:29,009 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-23_02-11-29.log] [testng] 02:11:29,009 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53d6095d - End of configuration. [testng] [2024-06-23 02:11:29,071] [pool-1-thread-10] Initializing /data/public/davemason/Convallaria_3C_10T_confocal.ims: [testng] 02:11:29,071 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:11:29,071 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:29,072 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-23_02-11-29.log] [testng] 02:11:29,072 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d3b8fa9 - End of configuration. [testng] [2024-06-23 02:11:29,097] [pool-1-thread-9] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal.ims: [testng] 02:11:29,097 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:11:29,098 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:29,099 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-23_02-11-29.log] [testng] 02:11:29,099 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5334ebbf - End of configuration. [testng] [2024-06-23 02:11:29,136] [pool-1-thread-8] Initializing /data/public/davemason/TransFactors_2C_34Z_SRRF_IMS3.ims: [testng] 02:11:29,137 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:11:29,137 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:29,138 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-23_02-11-29.log] [testng] 02:11:29,138 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3cffb9f8 - End of configuration. [testng] [2024-06-23 02:11:29,165] [pool-1-thread-7] Initializing /data/qa-17839/Fusion _Stack.ims: [testng] 02:11:29,166 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:11:29,166 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:29,167 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-23_02-11-29.log] [testng] 02:11:29,167 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5260a8b - End of configuration. [testng] [2024-06-23 02:11:29,218] [pool-1-thread-6] Initializing /data/generated/10-31_E_t0014.ims: [testng] 02:11:29,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:11:29,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:29,220 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-23_02-11-29.log] [testng] 02:11:29,220 |-INFO in ch.qos.logback.core.sift.SiftProcessor@245814c0 - End of configuration. [testng] [2024-06-23 02:11:29,237] [pool-1-thread-5] Initializing /data/jason/imaris_5_5_demoimages/PtK2Cell.ims: [testng] 02:11:29,237 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:11:29,237 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:29,238 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-23_02-11-29.log] [testng] 02:11:29,238 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e35f24a - End of configuration. [testng] [2024-06-23 02:11:29,269] [pool-1-thread-4] Initializing /data/jake/p75Cherry M2 010-3~B.ims: [testng] 02:11:29,270 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:11:29,270 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:29,271 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-23_02-11-29.log] [testng] 02:11:29,271 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f2b66c7 - End of configuration. [testng] [2024-06-23 02:11:29,310] [pool-1-thread-3] Initializing /data/qa-17515/Organoid=1.ims: [testng] 02:11:29,310 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:11:29,310 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:29,311 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-23_02-11-29.log] [testng] 02:11:29,312 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b94360b - End of configuration. [testng] [2024-06-23 02:11:29,390] [pool-1-thread-2] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal_IMS3.ims: [testng] 02:11:29,391 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:11:29,391 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:29,392 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-23_02-11-29.log] [testng] 02:11:29,393 |-INFO in ch.qos.logback.core.sift.SiftProcessor@295b69ee - End of configuration. BUILD SUCCESSFUL Total time: 2 minutes 58 seconds Finished: SUCCESS