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Started by upstream project "BIOFORMATS-test-repo" build number 90 originally caused by: Started by upstream project "Trigger" build number 101 originally caused by: Started by timer 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/jenkins822571928432799034.sh + '[' nifti = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_13898_merge_ci -v /uod/idr/repos/curated/nifti:/data -v /uod/idr-scratch/merge-ci/curated/nifti:/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] 02:41:01,149 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:41:01,150 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 02:41:01,150 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:41:01,151 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:41:01,151 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:41:01,152 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:41:01,152 |-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] 02:41:01,152 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:41:01,152 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:41:01,153 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:41:01,153 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:41:01,153 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:41:01,317 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:41:01,317 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:41:01,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:41:01,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:41:01,345 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:41:01,345 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:41:01,345 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:41:01,345 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:41:01,345 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 02:41:01,346 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 02:41:01,346 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 194 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-12 02:41:01,356] [main] java.version = 17.0.2 [testng] 02:41:01,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:41:01,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:01,401 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-12_02-41-01.log] [testng] 02:41:01,403 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-06-12 02:41:01,406] [main] testng.directory = /data [testng] [2024-06-12 02:41:01,407] [main] testng.configDirectory = /config [testng] [2024-06-12 02:41:01,420] [main] testng.multiplier = 1.0 [testng] [2024-06-12 02:41:01,421] [main] testng.in-memory = false [testng] [2024-06-12 02:41:01,421] [main] testng.allow-missing = false [testng] [2024-06-12 02:41:01,421] [main] user.language = en [testng] [2024-06-12 02:41:01,422] [main] user.country = ${user.country} [testng] [2024-06-12 02:41:01,422] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-12 02:41:02,169] [main] ---------------------------------------- [testng] [2024-06-12 02:41:02,169] [main] Total files: 23 [testng] [2024-06-12 02:41:02,169] [main] Scan time: 0.747 s (32 ms/file) [testng] [2024-06-12 02:41:02,169] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-12 02:41:06,846] [pool-1-thread-1] Initializing /data/public/NIH/avg152T1_LR_nifti.nii.gz: [testng] 02:41:06,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:41:06,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:06,848 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-12_02-41-06.log] [testng] 02:41:06,849 |-INFO in ch.qos.logback.core.sift.SiftProcessor@86a3820 - End of configuration. [testng] [2024-06-12 02:41:07,086] [pool-1-thread-12] Initializing /data/public/NIH/avg152T1_RL_nifti.nii.gz: [testng] 02:41:07,086 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:41:07,086 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:07,088 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-12_02-41-07.log] [testng] 02:41:07,088 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b4efa30 - End of configuration. [testng] [2024-06-12 02:41:07,280] [pool-1-thread-11] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_100.hdr: [testng] 02:41:07,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:41:07,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:07,281 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-12_02-41-07.log] [testng] 02:41:07,282 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55d671a9 - End of configuration. [testng] [2024-06-12 02:41:07,297] [pool-1-thread-10] Initializing /data/public/NIH/avg152T1_RL_nifti.nii: [testng] 02:41:07,297 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:41:07,297 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:07,297 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-12_02-41-07.log] [testng] 02:41:07,298 |-INFO in ch.qos.logback.core.sift.SiftProcessor@413d4520 - End of configuration. [testng] [2024-06-12 02:41:07,328] [pool-1-thread-9] Initializing /data/qa-17334/volume4d.nii: [testng] 02:41:07,329 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:41:07,329 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:07,330 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-12_02-41-07.log] [testng] 02:41:07,330 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ceb7e98 - End of configuration. [testng] [2024-06-12 02:41:07,354] [pool-1-thread-8] Initializing /data/public/NIH/newsirp_final_XML.nii: [testng] 02:41:07,355 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:41:07,355 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:07,356 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-12_02-41-07.log] [testng] 02:41:07,356 |-INFO in ch.qos.logback.core.sift.SiftProcessor@756a3221 - End of configuration. [testng] [2024-06-12 02:41:07,378] [pool-1-thread-7] Initializing /data/public/NIH/minimal.hdr: [testng] 02:41:07,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:41:07,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:07,379 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-12_02-41-07.log] [testng] 02:41:07,379 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3881e622 - End of configuration. [testng] [2024-06-12 02:41:07,391] [pool-1-thread-6] Initializing /data/public/NIH/avg152T1_LR_nifti.nii: [testng] 02:41:07,391 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:41:07,391 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:07,392 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-12_02-41-07.log] [testng] 02:41:07,392 |-INFO in ch.qos.logback.core.sift.SiftProcessor@865a50f - End of configuration. [testng] [2024-06-12 02:41:07,417] [pool-1-thread-5] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_94.hdr: [testng] 02:41:07,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:41:07,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:07,418 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-12_02-41-07.log] [testng] 02:41:07,418 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7664b379 - End of configuration. [testng] [2024-06-12 02:41:07,429] [pool-1-thread-4] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_94.hdr: [testng] 02:41:07,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:41:07,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:07,430 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-12_02-41-07.log] [testng] 02:41:07,431 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a01c82 - End of configuration. [testng] [2024-06-12 02:41:07,441] [pool-1-thread-3] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_100.hdr: [testng] 02:41:07,441 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:41:07,441 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:07,442 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-12_02-41-07.log] [testng] 02:41:07,443 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ae91554 - End of configuration. [testng] [2024-06-12 02:41:07,456] [pool-1-thread-2] Initializing /data/public/NIH/minimal.nii: [testng] 02:41:07,456 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:41:07,456 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:41:07,457 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-12_02-41-07.log] [testng] 02:41:07,457 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27f2047b - End of configuration. [testng] [2024-06-12 02:41:08,846] [pool-1-thread-2] Initializing /data/public/NIH/zstat1.nii.gz: [testng] [2024-06-12 02:41:08,928] [pool-1-thread-6] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_26_conf_91.hdr: [testng] [2024-06-12 02:41:08,945] [pool-1-thread-3] Initializing /data/public/NIH/filtered_func_data.nii: [testng] [2024-06-12 02:41:08,964] [pool-1-thread-5] Initializing /data/public/NIH/filtered_func_data.nii.gz: [testng] [2024-06-12 02:41:11,527] [pool-1-thread-4] Initializing /data/public/NIH/zstat1.nii: [testng] [2024-06-12 02:41:11,537] [pool-1-thread-9] Initializing /data/public/NIH/avg152T1_LR_nifti.hdr: [testng] [2024-06-12 02:41:11,546] [pool-1-thread-11] Initializing /data/public/NIH/avg152T1_RL_nifti.hdr: [testng] [2024-06-12 02:41:11,555] [pool-1-thread-8] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_27_conf_86.hdr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1060, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 39 seconds Finished: SUCCESS