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Started by upstream project "BIOFORMATS-test-repo" build number 300 originally caused by: Started by upstream project "Trigger" build number 322 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins14424750416370177246.sh + '[' nifti = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_47547_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 test-automated: [testng] File leak detector installed [testng] 05:37:18,749 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 05:37:18,751 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 05:37:18,751 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:37:18,752 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:37:18,752 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 05:37:18,752 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 05:37:18,752 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 05:37:18,752 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:37:18,753 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:37:18,753 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 05:37:18,753 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 05:37:18,753 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 05:37:18,966 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 05:37:18,966 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 05:37:18,992 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 05:37:18,993 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 05:37:19,000 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 05:37:19,000 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 05:37:19,000 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 05:37:19,001 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 05:37:19,001 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 05:37:19,002 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 05:37:19,002 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 249 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-27 05:37:19,011] [main] java.version = 1.8.0_342 [testng] 05:37:19,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:37:19,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:37:19,058 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-27_05-37-19.log] [testng] 05:37:19,059 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-27 05:37:19,061] [main] testng.directory = /data [testng] [2024-12-27 05:37:19,061] [main] testng.configDirectory = /config [testng] [2024-12-27 05:37:19,073] [main] testng.multiplier = 1.0 [testng] [2024-12-27 05:37:19,073] [main] testng.in-memory = false [testng] [2024-12-27 05:37:19,073] [main] testng.allow-missing = false [testng] [2024-12-27 05:37:19,073] [main] user.language = en [testng] [2024-12-27 05:37:19,073] [main] user.country = ${user.country} [testng] [2024-12-27 05:37:19,073] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-27 05:37:41,282] [main] ---------------------------------------- [testng] [2024-12-27 05:37:41,282] [main] Total files: 23 [testng] [2024-12-27 05:37:41,282] [main] Scan time: 22.209 s (965 ms/file) [testng] [2024-12-27 05:37:41,283] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-27 05:38:37,303] [pool-1-thread-1] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_100.hdr: [testng] 05:38:37,304 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 05:38:37,304 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:38:37,305 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-27_05-38-37.log] [testng] 05:38:37,306 |-INFO in ch.qos.logback.core.sift.SiftProcessor@153f2da5 - End of configuration. [testng] [2024-12-27 05:38:38,647] [pool-1-thread-12] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_100.hdr: [testng] 05:38:38,647 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 05:38:38,647 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:38:38,648 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-27_05-38-38.log] [testng] 05:38:38,648 |-INFO in ch.qos.logback.core.sift.SiftProcessor@598715dd - End of configuration. [testng] [2024-12-27 05:38:39,954] [pool-1-thread-11] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_26_conf_91.hdr: [testng] 05:38:39,954 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 05:38:39,954 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:38:39,955 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-27_05-38-39.log] [testng] 05:38:39,955 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45bd5b4 - End of configuration. [testng] [2024-12-27 05:38:41,235] [pool-1-thread-10] Initializing /data/public/NIH/zstat1.nii: [testng] 05:38:41,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 05:38:41,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:38:41,236 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-27_05-38-41.log] [testng] 05:38:41,237 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f89465d - End of configuration. [testng] [2024-12-27 05:38:42,502] [pool-1-thread-9] Initializing /data/public/NIH/avg152T1_RL_nifti.nii: [testng] 05:38:42,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 05:38:42,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:38:42,503 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-27_05-38-42.log] [testng] 05:38:42,503 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55a859f0 - End of configuration. [testng] [2024-12-27 05:38:43,753] [pool-1-thread-8] Initializing /data/public/NIH/avg152T1_LR_nifti.hdr: [testng] 05:38:43,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 05:38:43,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:38:43,754 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-27_05-38-43.log] [testng] 05:38:43,755 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ddc88e2 - End of configuration. [testng] [2024-12-27 05:38:45,130] [pool-1-thread-7] Initializing /data/public/NIH/filtered_func_data.nii: [testng] 05:38:45,131 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 05:38:45,131 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:38:45,131 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-27_05-38-45.log] [testng] 05:38:45,132 |-INFO in ch.qos.logback.core.sift.SiftProcessor@284002f2 - End of configuration. [testng] [2024-12-27 05:38:46,378] [pool-1-thread-6] Initializing /data/public/NIH/minimal.hdr: [testng] 05:38:46,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 05:38:46,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:38:46,379 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-27_05-38-46.log] [testng] 05:38:46,379 |-INFO in ch.qos.logback.core.sift.SiftProcessor@691ef92b - End of configuration. [testng] [2024-12-27 05:38:47,728] [pool-1-thread-5] Initializing /data/public/NIH/avg152T1_LR_nifti.nii: [testng] 05:38:47,729 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 05:38:47,729 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:38:47,729 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-27_05-38-47.log] [testng] 05:38:47,730 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f8a175d - End of configuration. [testng] [2024-12-27 05:38:48,992] [pool-1-thread-4] Initializing /data/public/NIH/zstat1.nii.gz: [testng] 05:38:48,992 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 05:38:48,992 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:38:48,993 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-27_05-38-48.log] [testng] 05:38:48,993 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67d96332 - End of configuration. [testng] [2024-12-27 05:38:54,180] [pool-1-thread-3] Initializing /data/public/NIH/avg152T1_RL_nifti.nii.gz: [testng] 05:38:54,180 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 05:38:54,180 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:38:54,180 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-27_05-38-54.log] [testng] 05:38:54,181 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b611c35 - End of configuration. [testng] [2024-12-27 05:38:59,503] [pool-1-thread-2] Initializing /data/public/NIH/avg152T1_LR_nifti.nii.gz: [testng] 05:38:59,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 05:38:59,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:38:59,505 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-27_05-38-59.log] [testng] 05:38:59,505 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f9eccec - End of configuration. [testng] [2024-12-27 05:39:14,561] [pool-1-thread-9] Initializing /data/public/NIH/newsirp_final_XML.nii: [testng] [2024-12-27 05:39:15,871] [pool-1-thread-7] Initializing /data/public/NIH/avg152T1_RL_nifti.hdr: [testng] [2024-12-27 05:39:17,358] [pool-1-thread-10] Initializing /data/public/NIH/filtered_func_data.nii.gz: [testng] [2024-12-27 05:39:25,602] [pool-1-thread-5] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_94.hdr: [testng] [2024-12-27 05:39:30,778] [pool-1-thread-8] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_94.hdr: [testng] [2024-12-27 05:39:32,172] [pool-1-thread-6] Initializing /data/public/NIH/minimal.nii: [testng] [2024-12-27 05:39:33,437] [pool-1-thread-1] Initializing /data/qa-17334/volume4d.nii: [testng] [2024-12-27 05:39:34,698] [pool-1-thread-11] 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: 3 minutes 16 seconds Finished: SUCCESS