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Started by upstream project "BIOFORMATS-test-repo" build number 44 originally caused by: Started by upstream project "Trigger" build number 51 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins16618425902057826420.sh + '[' nifti = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_6354_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 02:38:48,637 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:38:48,638 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 02:38:48,638 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:38:48,640 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:38:48,640 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:38:48,640 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:38:48,641 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:38:48,641 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:38:48,641 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:38:48,642 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:38:48,642 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:38:48,642 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:38:48,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:38:48,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:38:48,828 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:38:48,828 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:38:48,834 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:38:48,835 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:38:48,835 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:38:48,835 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:38:48,835 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 02:38:48,836 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 02:38:48,836 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 195 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-25 02:38:48,846] [main] java.version = 21 [testng] 02:38:48,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:38:48,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:38:48,892 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-25_02-38-48.log] [testng] 02:38:48,894 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-04-25 02:38:48,895] [main] testng.directory = /data [testng] [2024-04-25 02:38:48,895] [main] testng.configDirectory = /config [testng] [2024-04-25 02:38:48,905] [main] testng.multiplier = 1.0 [testng] [2024-04-25 02:38:48,905] [main] testng.in-memory = false [testng] [2024-04-25 02:38:48,905] [main] testng.allow-missing = false [testng] [2024-04-25 02:38:48,905] [main] user.language = en [testng] [2024-04-25 02:38:48,905] [main] user.country = ${user.country} [testng] [2024-04-25 02:38:48,905] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-04-25 02:38:49,810] [main] ---------------------------------------- [testng] [2024-04-25 02:38:49,810] [main] Total files: 23 [testng] [2024-04-25 02:38:49,810] [main] Scan time: 0.904 s (39 ms/file) [testng] [2024-04-25 02:38:49,810] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-25 02:38:54,398] [pool-1-thread-1] Initializing /data/public/NIH/avg152T1_LR_nifti.hdr: [testng] 02:38:54,399 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:38:54,399 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:38:54,401 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-25_02-38-54.log] [testng] 02:38:54,401 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fb5db7 - End of configuration. [testng] [2024-04-25 02:38:54,424] [pool-1-thread-12] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_27_conf_86.hdr: [testng] 02:38:54,425 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:38:54,425 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:38:54,426 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-25_02-38-54.log] [testng] 02:38:54,434 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d9aa1ab - End of configuration. [testng] [2024-04-25 02:38:54,455] [pool-1-thread-11] Initializing /data/qa-17334/volume4d.nii: [testng] 02:38:54,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:38:54,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:38:54,456 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-25_02-38-54.log] [testng] 02:38:54,457 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a9073e7 - End of configuration. [testng] [2024-04-25 02:38:54,489] [pool-1-thread-10] Initializing /data/public/NIH/avg152T1_LR_nifti.nii.gz: [testng] 02:38:54,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:38:54,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:38:54,490 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-25_02-38-54.log] [testng] 02:38:54,490 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e49da5f - End of configuration. [testng] [2024-04-25 02:38:54,703] [pool-1-thread-9] Initializing /data/public/NIH/newsirp_final_XML.nii: [testng] 02:38:54,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:38:54,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:38:54,704 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-25_02-38-54.log] [testng] 02:38:54,705 |-INFO in ch.qos.logback.core.sift.SiftProcessor@501ff8a5 - End of configuration. [testng] [2024-04-25 02:38:54,732] [pool-1-thread-8] Initializing /data/public/NIH/minimal.nii: [testng] 02:38:54,732 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:38:54,733 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:38:54,733 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-25_02-38-54.log] [testng] 02:38:54,734 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2aeb0854 - End of configuration. [testng] [2024-04-25 02:38:54,744] [pool-1-thread-7] Initializing /data/public/NIH/avg152T1_RL_nifti.hdr: [testng] 02:38:54,744 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:38:54,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:38:54,745 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-25_02-38-54.log] [testng] 02:38:54,746 |-INFO in ch.qos.logback.core.sift.SiftProcessor@341d400d - End of configuration. [testng] [2024-04-25 02:38:54,775] [pool-1-thread-6] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_26_conf_91.hdr: [testng] 02:38:54,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:38:54,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:38:54,776 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-25_02-38-54.log] [testng] 02:38:54,776 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10ee589 - End of configuration. [testng] [2024-04-25 02:38:54,788] [pool-1-thread-5] Initializing /data/public/NIH/zstat1.nii: [testng] 02:38:54,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:38:54,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:38:54,789 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-25_02-38-54.log] [testng] 02:38:54,789 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e724045 - End of configuration. [testng] [2024-04-25 02:38:54,802] [pool-1-thread-4] Initializing /data/public/NIH/filtered_func_data.nii.gz: [testng] 02:38:54,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:38:54,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:38:54,803 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-25_02-38-54.log] [testng] 02:38:54,803 |-INFO in ch.qos.logback.core.sift.SiftProcessor@194c43ae - End of configuration. [testng] [2024-04-25 02:38:57,625] [pool-1-thread-3] Initializing /data/public/NIH/filtered_func_data.nii: [testng] 02:38:57,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:38:57,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:38:57,627 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-25_02-38-57.log] [testng] 02:38:57,628 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46233177 - End of configuration. [testng] [2024-04-25 02:38:57,652] [pool-1-thread-2] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_94.hdr: [testng] 02:38:57,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:38:57,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:38:57,653 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-25_02-38-57.log] [testng] 02:38:57,654 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28a44680 - End of configuration. [testng] [2024-04-25 02:38:58,983] [pool-1-thread-8] Initializing /data/public/NIH/avg152T1_LR_nifti.nii: [testng] [2024-04-25 02:38:59,000] [pool-1-thread-7] Initializing /data/public/NIH/avg152T1_RL_nifti.nii: [testng] [2024-04-25 02:38:59,017] [pool-1-thread-5] Initializing /data/public/NIH/avg152T1_RL_nifti.nii.gz: [testng] [2024-04-25 02:38:59,215] [pool-1-thread-6] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_100.hdr: [testng] [2024-04-25 02:38:59,225] [pool-1-thread-12] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_100.hdr: [testng] [2024-04-25 02:38:59,234] [pool-1-thread-11] Initializing /data/public/NIH/zstat1.nii.gz: [testng] [2024-04-25 02:38:59,310] [pool-1-thread-9] Initializing /data/public/NIH/minimal.hdr: [testng] [2024-04-25 02:38:59,321] [pool-1-thread-3] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_94.hdr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1060, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 38 seconds Finished: SUCCESS