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Started by upstream project "BIOFORMATS-test-repo" build number 241 originally caused by: Started by upstream project "Trigger" build number 266 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins651374050195406454.sh + '[' nifti = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_37989_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] 04:04:20,427 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 04:04:20,428 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 04:04:20,428 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:04:20,429 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:04:20,430 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 04:04:20,430 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 04:04:20,430 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 04:04:20,430 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:04:20,431 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:04:20,431 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 04:04:20,431 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 04:04:20,431 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 04:04:20,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 04:04:20,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 04:04:20,689 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 04:04:20,689 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 04:04:20,697 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 04:04:20,697 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 04:04:20,697 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 04:04:20,698 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 04:04:20,698 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 04:04:20,699 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 04:04:20,699 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 268 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-01 04:04:20,709] [main] java.version = 1.8.0_342 [testng] 04:04:20,712 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:04:20,712 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:04:20,757 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-01_04-04-20.log] [testng] 04:04:20,759 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-01 04:04:20,761] [main] testng.directory = /data [testng] [2024-11-01 04:04:20,761] [main] testng.configDirectory = /config [testng] [2024-11-01 04:04:20,773] [main] testng.multiplier = 1.0 [testng] [2024-11-01 04:04:20,773] [main] testng.in-memory = false [testng] [2024-11-01 04:04:20,773] [main] testng.allow-missing = false [testng] [2024-11-01 04:04:20,773] [main] user.language = en [testng] [2024-11-01 04:04:20,773] [main] user.country = ${user.country} [testng] [2024-11-01 04:04:20,773] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-01 04:04:30,263] [main] ---------------------------------------- [testng] [2024-11-01 04:04:30,263] [main] Total files: 23 [testng] [2024-11-01 04:04:30,263] [main] Scan time: 9.49 s (412 ms/file) [testng] [2024-11-01 04:04:30,263] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-01 04:04:54,662] [pool-1-thread-1] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_26_conf_91.hdr: [testng] 04:04:54,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 04:04:54,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:04:54,664 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-01_04-04-54.log] [testng] 04:04:54,664 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37326e47 - End of configuration. [testng] [2024-11-01 04:04:55,144] [pool-1-thread-12] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_100.hdr: [testng] 04:04:55,144 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 04:04:55,145 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:04:55,145 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-01_04-04-55.log] [testng] 04:04:55,146 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3734af7e - End of configuration. [testng] [2024-11-01 04:04:55,625] [pool-1-thread-11] Initializing /data/qa-17334/volume4d.nii: [testng] 04:04:55,625 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 04:04:55,625 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:04:55,626 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-01_04-04-55.log] [testng] 04:04:55,626 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69376478 - End of configuration. [testng] [2024-11-01 04:04:56,092] [pool-1-thread-10] Initializing /data/public/NIH/filtered_func_data.nii: [testng] 04:04:56,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 04:04:56,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:04:56,092 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-01_04-04-56.log] [testng] 04:04:56,093 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e5eb750 - End of configuration. [testng] [2024-11-01 04:04:56,536] [pool-1-thread-9] Initializing /data/public/NIH/avg152T1_LR_nifti.nii.gz: [testng] 04:04:56,536 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 04:04:56,537 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:04:56,537 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-01_04-04-56.log] [testng] 04:04:56,537 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bda8a8e - End of configuration. [testng] [2024-11-01 04:04:58,563] [pool-1-thread-8] Initializing /data/public/NIH/minimal.hdr: [testng] 04:04:58,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 04:04:58,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:04:58,564 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-01_04-04-58.log] [testng] 04:04:58,565 |-INFO in ch.qos.logback.core.sift.SiftProcessor@369d4db0 - End of configuration. [testng] [2024-11-01 04:04:59,025] [pool-1-thread-7] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_100.hdr: [testng] 04:04:59,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 04:04:59,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:04:59,026 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-01_04-04-59.log] [testng] 04:04:59,027 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e0775e7 - End of configuration. [testng] [2024-11-01 04:04:59,500] [pool-1-thread-6] Initializing /data/public/NIH/newsirp_final_XML.nii: [testng] 04:04:59,500 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:04:59,500 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:04:59,501 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-01_04-04-59.log] [testng] 04:04:59,501 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e146123 - End of configuration. [testng] [2024-11-01 04:04:59,942] [pool-1-thread-5] Initializing /data/public/NIH/avg152T1_RL_nifti.hdr: [testng] 04:04:59,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 04:04:59,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:04:59,943 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-01_04-04-59.log] [testng] 04:04:59,943 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71fc8728 - End of configuration. [testng] [2024-11-01 04:05:00,426] [pool-1-thread-4] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_94.hdr: [testng] 04:05:00,426 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 04:05:00,426 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:05:00,427 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-01_04-05-00.log] [testng] 04:05:00,427 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57a8a936 - End of configuration. [testng] [2024-11-01 04:05:00,895] [pool-1-thread-3] Initializing /data/public/NIH/filtered_func_data.nii.gz: [testng] 04:05:00,895 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 04:05:00,895 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:05:00,895 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-01_04-05-00.log] [testng] 04:05:00,896 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26ccd95a - End of configuration. [testng] [2024-11-01 04:05:05,548] [pool-1-thread-2] Initializing /data/public/NIH/avg152T1_RL_nifti.nii: [testng] 04:05:05,548 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:05:05,548 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:05:05,549 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-01_04-05-05.log] [testng] 04:05:05,549 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21675177 - End of configuration. [testng] [2024-11-01 04:05:09,961] [pool-1-thread-11] Initializing /data/public/NIH/avg152T1_LR_nifti.hdr: [testng] [2024-11-01 04:05:10,483] [pool-1-thread-2] Initializing /data/public/NIH/minimal.nii: [testng] [2024-11-01 04:05:10,997] [pool-1-thread-10] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_27_conf_86.hdr: [testng] [2024-11-01 04:05:11,485] [pool-1-thread-6] Initializing /data/public/NIH/zstat1.nii.gz: [testng] [2024-11-01 04:05:14,299] [pool-1-thread-8] Initializing /data/public/NIH/avg152T1_RL_nifti.nii.gz: [testng] [2024-11-01 04:05:16,500] [pool-1-thread-12] Initializing /data/public/NIH/zstat1.nii: [testng] [2024-11-01 04:05:17,069] [pool-1-thread-4] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_94.hdr: [testng] [2024-11-01 04:05:17,749] [pool-1-thread-1] Initializing /data/public/NIH/avg152T1_LR_nifti.nii: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1060, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 1 minute 31 seconds Finished: SUCCESS