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Started by upstream project "BIOFORMATS-test-repo" build number 184 originally caused by: Started by upstream project "Trigger" build number 206 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins16589893421920066471.sh + '[' imaris = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_29125_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] 11:33:58,136 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 11:33:58,138 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 11:33:58,138 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:33:58,139 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:33:58,139 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 11:33:58,140 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 11:33:58,140 |-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] 11:33:58,140 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:33:58,141 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:33:58,141 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 11:33:58,141 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:33:58,142 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:33:58,322 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:33:58,322 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:33:58,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:33:58,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:33:58,356 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:33:58,357 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:33:58,357 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:33:58,358 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:33:58,358 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 11:33:58,358 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 11:33:58,359 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 218 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-11 11:33:58,370] [main] java.version = 17.0.2 [testng] 11:33:58,375 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:33:58,375 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:33:58,424 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-11_11-33-58.log] [testng] 11:33:58,426 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-09-11 11:33:58,428] [main] testng.directory = /data [testng] [2024-09-11 11:33:58,428] [main] testng.configDirectory = /config [testng] [2024-09-11 11:33:58,439] [main] testng.multiplier = 1.0 [testng] [2024-09-11 11:33:58,440] [main] testng.in-memory = false [testng] [2024-09-11 11:33:58,441] [main] testng.allow-missing = false [testng] [2024-09-11 11:33:58,441] [main] user.language = en [testng] [2024-09-11 11:33:58,441] [main] user.country = ${user.country} [testng] [2024-09-11 11:33:58,441] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-09-11 11:34:06,959] [main] ---------------------------------------- [testng] [2024-09-11 11:34:06,959] [main] Total files: 68 [testng] [2024-09-11 11:34:06,959] [main] Scan time: 8.518 s (125 ms/file) [testng] [2024-09-11 11:34:06,959] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 60 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-11 11:34:27,724] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal.ims: [testng] 11:34:27,724 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 11:34:27,724 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:27,726 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-11_11-34-27.log] [testng] 11:34:27,726 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2385c777 - End of configuration. [testng] [2024-09-11 11:34:27,807] [pool-1-thread-12] Initializing /data/jason/imaris_5_5_demoimages/HeLaCell.ims: [testng] 11:34:27,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 11:34:27,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:27,808 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-11_11-34-27.log] [testng] 11:34:27,809 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3dc93b0a - End of configuration. [testng] [2024-09-11 11:34:27,886] [pool-1-thread-11] Initializing /data/generated/10-31_E_t0009.ims: [testng] 11:34:27,886 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 11:34:27,886 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:27,887 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-11_11-34-27.log] [testng] 11:34:27,888 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12778b73 - End of configuration. [testng] [2024-09-11 11:34:27,918] [pool-1-thread-10] Initializing /data/oliver/Stack2_8Bit.ims: [testng] 11:34:27,919 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 11:34:27,919 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:27,919 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-11_11-34-27.log] [testng] 11:34:27,920 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73f693c4 - End of configuration. [testng] [2024-09-11 11:34:28,006] [pool-1-thread-9] Initializing /data/james/apoEcherry_IL10GFP_tfn647_1_R3D_D3D-Display Adjustment-Save-2011-7-5-1.ims: [testng] 11:34:28,007 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 11:34:28,007 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:28,008 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-11_11-34-28.log] [testng] 11:34:28,008 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15c77b87 - End of configuration. [testng] [2024-09-11 11:34:28,066] [pool-1-thread-8] Initializing /data/public/davemason/Convallaria_3C_1T_2x2grid_confocal.ims: [testng] 11:34:28,066 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 11:34:28,066 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:28,067 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-11_11-34-28.log] [testng] 11:34:28,067 |-INFO in ch.qos.logback.core.sift.SiftProcessor@eff4946 - End of configuration. [testng] [2024-09-11 11:34:28,115] [pool-1-thread-7] Initializing /data/jason/imaris_5_5_demoimages/PyramidalCell.ims: [testng] 11:34:28,115 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 11:34:28,115 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:28,116 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-11_11-34-28.log] [testng] 11:34:28,116 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57e5b570 - End of configuration. [testng] [2024-09-11 11:34:28,186] [pool-1-thread-6] Initializing /data/generated/10-31_E_t0004.ims: [testng] 11:34:28,186 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 11:34:28,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:28,188 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-11_11-34-28.log] [testng] 11:34:28,188 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14701053 - End of configuration. [testng] [2024-09-11 11:34:28,248] [pool-1-thread-5] Initializing /data/generated/10-31_E_t0012.ims: [testng] 11:34:28,248 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 11:34:28,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:28,249 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-11_11-34-28.log] [testng] 11:34:28,250 |-INFO in ch.qos.logback.core.sift.SiftProcessor@689cf560 - End of configuration. [testng] [2024-09-11 11:34:28,280] [pool-1-thread-4] Initializing /data/public/davemason/TransFactors_2C_SRRF_IMS3.ims: [testng] 11:34:28,281 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 11:34:28,281 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:28,282 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-11_11-34-28.log] [testng] 11:34:28,283 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c23818d - End of configuration. [testng] [2024-09-11 11:34:28,326] [pool-1-thread-3] Initializing /data/generated/mri-stack-original.ims: [testng] 11:34:28,327 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 11:34:28,327 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:28,328 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-11_11-34-28.log] [testng] 11:34:28,328 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e80d0fa - End of configuration. [testng] [2024-09-11 11:34:28,345] [pool-1-thread-2] Initializing /data/jason/imaris_5_5_demoimages/retina.ims: [testng] 11:34:28,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 11:34:28,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:34:28,346 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-11_11-34-28.log] [testng] 11:34:28,346 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a5f55d - End of configuration. BUILD SUCCESSFUL Total time: 2 minutes 51 seconds Finished: SUCCESS