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Started by upstream project "BIOFORMATS-test-repo" build number 265 originally caused by: Started by upstream project "Trigger" build number 288 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins2690788496962050887.sh + '[' nifti = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_41925_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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 05:30:28,485 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 05:30:28,487 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 05:30:28,487 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:30:28,488 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:30:28,488 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 05:30:28,489 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 05:30:28,489 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 05:30:28,489 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:30:28,489 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:30:28,490 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 05:30:28,490 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 05:30:28,491 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 05:30:28,647 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 05:30:28,647 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 05:30:28,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 05:30:28,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 05:30:28,673 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 05:30:28,673 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 05:30:28,673 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 05:30:28,673 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 05:30:28,673 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 05:30:28,674 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 05:30:28,674 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 185 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-23 05:30:28,682] [main] java.version = 11.0.16 [testng] 05:30:28,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:30:28,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:30:28,725 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-23_05-30-28.log] [testng] 05:30:28,726 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-11-23 05:30:28,728] [main] testng.directory = /data [testng] [2024-11-23 05:30:28,728] [main] testng.configDirectory = /config [testng] [2024-11-23 05:30:28,737] [main] testng.multiplier = 1.0 [testng] [2024-11-23 05:30:28,738] [main] testng.in-memory = false [testng] [2024-11-23 05:30:28,738] [main] testng.allow-missing = false [testng] [2024-11-23 05:30:28,738] [main] user.language = en [testng] [2024-11-23 05:30:28,738] [main] user.country = ${user.country} [testng] [2024-11-23 05:30:28,738] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-23 05:30:48,978] [main] ---------------------------------------- [testng] [2024-11-23 05:30:48,978] [main] Total files: 23 [testng] [2024-11-23 05:30:48,978] [main] Scan time: 20.239 s (879 ms/file) [testng] [2024-11-23 05:30:48,979] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-23 05:31:42,360] [pool-1-thread-1] Initializing /data/public/NIH/avg152T1_LR_nifti.hdr: [testng] 05:31:42,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 05:31:42,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:31:42,363 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-23_05-31-42.log] [testng] 05:31:42,369 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b91a1b4 - End of configuration. [testng] [2024-11-23 05:31:43,571] [pool-1-thread-12] Initializing /data/public/NIH/avg152T1_LR_nifti.nii.gz: [testng] 05:31:43,571 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 05:31:43,572 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:31:43,573 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-23_05-31-43.log] [testng] 05:31:43,573 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1129a9c5 - End of configuration. [testng] [2024-11-23 05:31:48,275] [pool-1-thread-11] Initializing /data/qa-17334/volume4d.nii: [testng] 05:31:48,276 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 05:31:48,276 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:31:48,276 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-23_05-31-48.log] [testng] 05:31:48,277 |-INFO in ch.qos.logback.core.sift.SiftProcessor@453e2ce0 - End of configuration. [testng] [2024-11-23 05:31:49,368] [pool-1-thread-10] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_94.hdr: [testng] 05:31:49,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 05:31:49,369 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:31:49,369 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-23_05-31-49.log] [testng] 05:31:49,370 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35ce9a97 - End of configuration. [testng] [2024-11-23 05:31:50,557] [pool-1-thread-9] Initializing /data/public/NIH/filtered_func_data.nii: [testng] 05:31:50,557 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 05:31:50,557 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:31:50,557 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-23_05-31-50.log] [testng] 05:31:50,558 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22db1d47 - End of configuration. [testng] [2024-11-23 05:31:51,699] [pool-1-thread-8] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_100.hdr: [testng] 05:31:51,699 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 05:31:51,699 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:31:51,700 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-23_05-31-51.log] [testng] 05:31:51,700 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a555c79 - End of configuration. [testng] [2024-11-23 05:31:52,891] [pool-1-thread-7] Initializing /data/public/NIH/zstat1.nii.gz: [testng] 05:31:52,891 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 05:31:52,891 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:31:52,892 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-23_05-31-52.log] [testng] 05:31:52,893 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f548562 - End of configuration. [testng] [2024-11-23 05:31:57,559] [pool-1-thread-6] Initializing /data/public/NIH/avg152T1_RL_nifti.hdr: [testng] 05:31:57,560 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 05:31:57,560 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:31:57,561 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-23_05-31-57.log] [testng] 05:31:57,561 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ba6bd9b - End of configuration. [testng] [2024-11-23 05:31:58,773] [pool-1-thread-5] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_27_conf_86.hdr: [testng] 05:31:58,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 05:31:58,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:31:58,774 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-23_05-31-58.log] [testng] 05:31:58,774 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8f0d8da - End of configuration. [testng] [2024-11-23 05:31:59,962] [pool-1-thread-4] Initializing /data/public/NIH/avg152T1_RL_nifti.nii: [testng] 05:31:59,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 05:31:59,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:31:59,963 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-23_05-31-59.log] [testng] 05:31:59,963 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4455ff72 - End of configuration. [testng] [2024-11-23 05:32:01,066] [pool-1-thread-3] Initializing /data/public/NIH/newsirp_final_XML.nii: [testng] 05:32:01,066 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 05:32:01,066 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:32:01,067 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-23_05-32-01.log] [testng] 05:32:01,067 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15d6e7a2 - End of configuration. [testng] [2024-11-23 05:32:02,173] [pool-1-thread-2] Initializing /data/public/NIH/minimal.nii: [testng] 05:32:02,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 05:32:02,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:32:02,173 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-23_05-32-02.log] [testng] 05:32:02,174 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35d551d9 - End of configuration. [testng] [2024-11-23 05:32:12,456] [pool-1-thread-2] Initializing /data/public/NIH/minimal.hdr: [testng] [2024-11-23 05:32:13,763] [pool-1-thread-11] Initializing /data/public/NIH/avg152T1_LR_nifti.nii: [testng] [2024-11-23 05:32:15,035] [pool-1-thread-4] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_94.hdr: [testng] [2024-11-23 05:32:16,277] [pool-1-thread-3] Initializing /data/public/NIH/avg152T1_RL_nifti.nii.gz: [testng] [2024-11-23 05:32:21,102] [pool-1-thread-9] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_26_conf_91.hdr: [testng] [2024-11-23 05:32:24,080] [pool-1-thread-1] Initializing /data/public/NIH/filtered_func_data.nii.gz: [testng] [2024-11-23 05:32:31,487] [pool-1-thread-8] Initializing /data/public/NIH/zstat1.nii: [testng] [2024-11-23 05:32:32,727] [pool-1-thread-5] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_100.hdr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1060, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 3 minutes 3 seconds Finished: SUCCESS