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Started by upstream project "BIOFORMATS-test-repo" build number 132 originally caused by: Started by upstream project "Trigger" build number 152 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins9724401195135601735.sh + '[' imaris = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_20754_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings 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] 11:51:10,940 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 11:51:10,942 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 11:51:10,942 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:51:10,943 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:51:10,943 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 11:51:10,943 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 11:51:10,944 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 11:51:10,944 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:51:10,944 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:51:10,945 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 11:51:10,945 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:51:10,945 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:51:11,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:51:11,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:51:11,134 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:51:11,134 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:51:11,140 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:51:11,141 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:51:11,141 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:51:11,141 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:51:11,141 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 11:51:11,142 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 11:51:11,142 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 198 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-25 11:51:11,151] [main] java.version = 21 [testng] 11:51:11,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:51:11,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:51:11,195 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-25_11-51-11.log] [testng] 11:51:11,196 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-07-25 11:51:11,198] [main] testng.directory = /data [testng] [2024-07-25 11:51:11,198] [main] testng.configDirectory = /config [testng] [2024-07-25 11:51:11,206] [main] testng.multiplier = 1.0 [testng] [2024-07-25 11:51:11,207] [main] testng.in-memory = false [testng] [2024-07-25 11:51:11,207] [main] testng.allow-missing = false [testng] [2024-07-25 11:51:11,207] [main] user.language = en [testng] [2024-07-25 11:51:11,207] [main] user.country = ${user.country} [testng] [2024-07-25 11:51:11,207] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-25 11:51:18,087] [main] ---------------------------------------- [testng] [2024-07-25 11:51:18,087] [main] Total files: 68 [testng] [2024-07-25 11:51:18,087] [main] Scan time: 6.88 s (101 ms/file) [testng] [2024-07-25 11:51:18,087] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 60 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-25 11:51:39,757] [pool-1-thread-1] Initializing /data/jason/imaris_5_5_demoimages/R18Demo.ims: [testng] 11:51:39,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 11:51:39,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:51:39,758 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-25_11-51-39.log] [testng] 11:51:39,759 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f61855c - End of configuration. [testng] [2024-07-25 11:51:39,801] [pool-1-thread-12] Initializing /data/qa-17522/2016-07-26_17.11.03_Sample Prefix_5P298C2_Protocol.ims: [testng] 11:51:39,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 11:51:39,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:51:39,802 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-25_11-51-39.log] [testng] 11:51:39,802 |-INFO in ch.qos.logback.core.sift.SiftProcessor@481ca5ff - End of configuration. [testng] [2024-07-25 11:51:39,866] [pool-1-thread-11] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal_deconvolved.ims: [testng] 11:51:39,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 11:51:39,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:51:39,867 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-25_11-51-39.log] [testng] 11:51:39,868 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6cdc1e76 - End of configuration. [testng] [2024-07-25 11:51:39,892] [pool-1-thread-10] Initializing /data/public/davemason/Convallaria_3C_10T_confocal.ims: [testng] 11:51:39,892 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 11:51:39,892 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:51:39,893 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-25_11-51-39.log] [testng] 11:51:39,893 |-INFO in ch.qos.logback.core.sift.SiftProcessor@475a5075 - End of configuration. [testng] [2024-07-25 11:51:39,916] [pool-1-thread-9] Initializing /data/public/davemason/Convallaria_3C_1T_2x2grid_confocal.ims: [testng] 11:51:39,916 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 11:51:39,917 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:51:39,917 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-25_11-51-39.log] [testng] 11:51:39,918 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40e8d183 - End of configuration. [testng] [2024-07-25 11:51:39,959] [pool-1-thread-8] Initializing /data/generated/10-31_E_t0015.ims: [testng] 11:51:39,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 11:51:39,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:51:39,960 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-25_11-51-39.log] [testng] 11:51:39,960 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48fbe31 - End of configuration. [testng] [2024-07-25 11:51:39,973] [pool-1-thread-7] Initializing /data/qa-4898/o383_1_457_CS_r1.ims: [testng] 11:51:39,974 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 11:51:39,974 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:51:39,974 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-25_11-51-39.log] [testng] 11:51:39,975 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e32f9bf - End of configuration. [testng] [2024-07-25 11:51:40,030] [pool-1-thread-6] Initializing /data/generated/10-31_E_t0009.ims: [testng] 11:51:40,030 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 11:51:40,030 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:51:40,031 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-25_11-51-40.log] [testng] 11:51:40,031 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e22d819 - End of configuration. [testng] [2024-07-25 11:51:40,042] [pool-1-thread-5] Initializing /data/jcb/fig 6B GFP-AP-2d.ims: [testng] 11:51:40,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 11:51:40,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:51:40,043 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-25_11-51-40.log] [testng] 11:51:40,043 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c9e9cb - End of configuration. [testng] [2024-07-25 11:51:40,072] [pool-1-thread-4] Initializing /data/jason/imaris_5_5_demoimages/retina.ims: [testng] 11:51:40,073 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 11:51:40,073 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:51:40,073 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-25_11-51-40.log] [testng] 11:51:40,074 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5169cb0f - End of configuration. [testng] [2024-07-25 11:51:40,108] [pool-1-thread-3] Initializing /data/public/davemason/TransFactors_2C_SRRF_IMS3.ims: [testng] 11:51:40,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 11:51:40,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:51:40,109 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-25_11-51-40.log] [testng] 11:51:40,109 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ca20aa8 - End of configuration. [testng] [2024-07-25 11:51:40,135] [pool-1-thread-2] Initializing /data/public/davemason/Convallaria_3C_1T_2x2grid_confocal_IMS3.ims: [testng] 11:51:40,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 11:51:40,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:51:40,136 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-25_11-51-40.log] [testng] 11:51:40,137 |-INFO in ch.qos.logback.core.sift.SiftProcessor@633132f5 - End of configuration. BUILD SUCCESSFUL Total time: 2 minutes 14 seconds Finished: SUCCESS