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Started by upstream project "BIOFORMATS-test-repo" build number 218 originally caused by: Started by upstream project "Trigger" build number 245 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins16426485209007659487.sh + '[' nifti = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_34681_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] 09:03:58,656 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 09:03:58,658 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 09:03:58,658 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:03:58,659 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:03:58,659 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 09:03:58,659 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 09:03:58,660 |-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] 09:03:58,660 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:03:58,660 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:03:58,661 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 09:03:58,661 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 09:03:58,661 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 09:03:58,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 09:03:58,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 09:03:58,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 09:03:58,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 09:03:58,858 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 09:03:58,858 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 09:03:58,858 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 09:03:58,859 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 09:03:58,859 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 09:03:58,860 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 09:03:58,860 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 200 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-12 09:03:58,868] [main] java.version = 11.0.16 [testng] 09:03:58,871 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 09:03:58,871 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:03:58,912 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-12_09-03-58.log] [testng] 09:03:58,913 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-12 09:03:58,915] [main] testng.directory = /data [testng] [2024-10-12 09:03:58,915] [main] testng.configDirectory = /config [testng] [2024-10-12 09:03:58,924] [main] testng.multiplier = 1.0 [testng] [2024-10-12 09:03:58,925] [main] testng.in-memory = false [testng] [2024-10-12 09:03:58,926] [main] testng.allow-missing = false [testng] [2024-10-12 09:03:58,926] [main] user.language = en [testng] [2024-10-12 09:03:58,926] [main] user.country = ${user.country} [testng] [2024-10-12 09:03:58,926] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-12 09:04:15,656] [main] ---------------------------------------- [testng] [2024-10-12 09:04:15,657] [main] Total files: 23 [testng] [2024-10-12 09:04:15,657] [main] Scan time: 16.73 s (727 ms/file) [testng] [2024-10-12 09:04:15,657] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-12 09:04:55,863] [pool-1-thread-1] Initializing /data/public/NIH/avg152T1_LR_nifti.hdr: [testng] 09:04:55,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 09:04:55,865 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:04:55,867 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-12_09-04-55.log] [testng] 09:04:55,867 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e922f72 - End of configuration. [testng] [2024-10-12 09:04:56,762] [pool-1-thread-12] Initializing /data/public/NIH/avg152T1_LR_nifti.nii.gz: [testng] 09:04:56,762 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 09:04:56,762 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:04:56,763 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-12_09-04-56.log] [testng] 09:04:56,764 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22bacd66 - End of configuration. [testng] [2024-10-12 09:05:00,476] [pool-1-thread-11] Initializing /data/qa-17334/volume4d.nii: [testng] 09:05:00,476 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 09:05:00,476 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:05:00,477 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-12_09-05-00.log] [testng] 09:05:00,477 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2658ef15 - End of configuration. [testng] [2024-10-12 09:05:01,306] [pool-1-thread-10] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_94.hdr: [testng] 09:05:01,306 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 09:05:01,306 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:05:01,307 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-12_09-05-01.log] [testng] 09:05:01,307 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7853b362 - End of configuration. [testng] [2024-10-12 09:05:02,207] [pool-1-thread-9] Initializing /data/public/NIH/filtered_func_data.nii: [testng] 09:05:02,207 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 09:05:02,207 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:05:02,208 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-12_09-05-02.log] [testng] 09:05:02,208 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67c496bc - End of configuration. [testng] [2024-10-12 09:05:03,028] [pool-1-thread-8] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_100.hdr: [testng] 09:05:03,028 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 09:05:03,028 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:05:03,028 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-12_09-05-03.log] [testng] 09:05:03,029 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1bf1d6ac - End of configuration. [testng] [2024-10-12 09:05:03,914] [pool-1-thread-7] Initializing /data/public/NIH/zstat1.nii.gz: [testng] 09:05:03,914 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 09:05:03,914 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:05:03,915 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-12_09-05-03.log] [testng] 09:05:03,915 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3fd98929 - End of configuration. [testng] [2024-10-12 09:05:07,480] [pool-1-thread-6] Initializing /data/public/NIH/avg152T1_RL_nifti.hdr: [testng] 09:05:07,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 09:05:07,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:05:07,481 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-12_09-05-07.log] [testng] 09:05:07,482 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18c727d1 - End of configuration. [testng] [2024-10-12 09:05:08,380] [pool-1-thread-5] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_27_conf_86.hdr: [testng] 09:05:08,380 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 09:05:08,381 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:05:08,381 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-12_09-05-08.log] [testng] 09:05:08,381 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4db1ade - End of configuration. [testng] [2024-10-12 09:05:09,274] [pool-1-thread-4] Initializing /data/public/NIH/avg152T1_RL_nifti.nii: [testng] 09:05:09,274 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 09:05:09,274 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:05:09,275 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-12_09-05-09.log] [testng] 09:05:09,275 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17f994b7 - End of configuration. [testng] [2024-10-12 09:05:10,122] [pool-1-thread-3] Initializing /data/public/NIH/newsirp_final_XML.nii: [testng] 09:05:10,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 09:05:10,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:05:10,123 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-12_09-05-10.log] [testng] 09:05:10,123 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31609622 - End of configuration. [testng] [2024-10-12 09:05:10,961] [pool-1-thread-2] Initializing /data/public/NIH/minimal.nii: [testng] 09:05:10,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 09:05:10,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:05:10,962 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-12_09-05-10.log] [testng] 09:05:10,962 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61b2da90 - End of configuration. [testng] [2024-10-12 09:05:18,109] [pool-1-thread-2] Initializing /data/public/NIH/minimal.hdr: [testng] [2024-10-12 09:05:19,009] [pool-1-thread-4] Initializing /data/public/NIH/avg152T1_LR_nifti.nii: [testng] [2024-10-12 09:05:19,879] [pool-1-thread-11] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_94.hdr: [testng] [2024-10-12 09:05:20,788] [pool-1-thread-9] Initializing /data/public/NIH/avg152T1_RL_nifti.nii.gz: [testng] [2024-10-12 09:05:24,301] [pool-1-thread-3] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_26_conf_91.hdr: [testng] [2024-10-12 09:05:27,755] [pool-1-thread-6] Initializing /data/public/NIH/filtered_func_data.nii.gz: [testng] [2024-10-12 09:05:33,843] [pool-1-thread-1] Initializing /data/public/NIH/zstat1.nii: [testng] [2024-10-12 09:05:34,701] [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: 2 minutes 25 seconds Finished: SUCCESS