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Started by upstream project "BIOFORMATS-test-repo" build number 282 originally caused by: Started by user devspace 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/jenkins14134217071816502035.sh + '[' nifti = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_44586_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] 13:50:08,374 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 13:50:08,376 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 13:50:08,376 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 13:50:08,377 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 13:50:08,377 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 13:50:08,377 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 13:50:08,378 |-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] 13:50:08,378 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 13:50:08,378 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 13:50:08,379 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 13:50:08,379 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 13:50:08,379 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 13:50:08,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 13:50:08,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 13:50:08,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 13:50:08,651 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 13:50:08,661 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 13:50:08,661 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 13:50:08,661 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 13:50:08,661 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 13:50:08,661 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 13:50:08,662 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 13:50:08,662 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 284 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-06 13:50:08,673] [main] java.version = 1.8.0_342 [testng] 13:50:08,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 13:50:08,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:50:08,730 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-06_13-50-08.log] [testng] 13:50:08,733 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-06 13:50:08,736] [main] testng.directory = /data [testng] [2024-12-06 13:50:08,736] [main] testng.configDirectory = /config [testng] [2024-12-06 13:50:08,752] [main] testng.multiplier = 1.0 [testng] [2024-12-06 13:50:08,752] [main] testng.in-memory = false [testng] [2024-12-06 13:50:08,752] [main] testng.allow-missing = false [testng] [2024-12-06 13:50:08,752] [main] user.language = en [testng] [2024-12-06 13:50:08,752] [main] user.country = ${user.country} [testng] [2024-12-06 13:50:08,752] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-06 13:50:23,398] [main] ---------------------------------------- [testng] [2024-12-06 13:50:23,399] [main] Total files: 23 [testng] [2024-12-06 13:50:23,399] [main] Scan time: 14.646 s (636 ms/file) [testng] [2024-12-06 13:50:23,399] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-06 13:50:57,885] [pool-1-thread-1] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_26_conf_91.hdr: [testng] 13:50:57,885 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 13:50:57,886 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:50:57,887 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-06_13-50-57.log] [testng] 13:50:57,888 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1acc5c74 - End of configuration. [testng] [2024-12-06 13:50:59,114] [pool-1-thread-12] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_100.hdr: [testng] 13:50:59,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 13:50:59,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:50:59,115 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-06_13-50-59.log] [testng] 13:50:59,115 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35dbe478 - End of configuration. [testng] [2024-12-06 13:50:59,744] [pool-1-thread-11] Initializing /data/qa-17334/volume4d.nii: [testng] 13:50:59,744 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 13:50:59,744 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:50:59,745 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-06_13-50-59.log] [testng] 13:50:59,745 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6aebd91b - End of configuration. [testng] [2024-12-06 13:51:00,919] [pool-1-thread-10] Initializing /data/public/NIH/filtered_func_data.nii: [testng] 13:51:00,919 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 13:51:00,919 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:51:00,920 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-06_13-51-00.log] [testng] 13:51:00,920 |-INFO in ch.qos.logback.core.sift.SiftProcessor@441ac4ee - End of configuration. [testng] [2024-12-06 13:51:01,502] [pool-1-thread-9] Initializing /data/public/NIH/avg152T1_LR_nifti.nii.gz: [testng] 13:51:01,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 13:51:01,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:51:01,503 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-06_13-51-01.log] [testng] 13:51:01,503 |-INFO in ch.qos.logback.core.sift.SiftProcessor@453b4616 - End of configuration. [testng] [2024-12-06 13:51:04,728] [pool-1-thread-8] Initializing /data/public/NIH/minimal.hdr: [testng] 13:51:04,728 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 13:51:04,728 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:51:04,729 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-06_13-51-04.log] [testng] 13:51:04,729 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9ea5c19 - End of configuration. [testng] [2024-12-06 13:51:05,384] [pool-1-thread-7] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_100.hdr: [testng] 13:51:05,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 13:51:05,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:51:05,385 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-06_13-51-05.log] [testng] 13:51:05,385 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56a8ce36 - End of configuration. [testng] [2024-12-06 13:51:06,036] [pool-1-thread-6] Initializing /data/public/NIH/newsirp_final_XML.nii: [testng] 13:51:06,036 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 13:51:06,036 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:51:06,037 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-06_13-51-06.log] [testng] 13:51:06,037 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ca6e55 - End of configuration. [testng] [2024-12-06 13:51:06,686] [pool-1-thread-5] Initializing /data/public/NIH/avg152T1_RL_nifti.hdr: [testng] 13:51:06,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 13:51:06,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:51:06,687 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-06_13-51-06.log] [testng] 13:51:06,688 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4286a6f2 - End of configuration. [testng] [2024-12-06 13:51:07,338] [pool-1-thread-4] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_94.hdr: [testng] 13:51:07,338 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 13:51:07,338 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:51:07,339 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-06_13-51-07.log] [testng] 13:51:07,339 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7cdf62cd - End of configuration. [testng] [2024-12-06 13:51:07,961] [pool-1-thread-3] Initializing /data/public/NIH/filtered_func_data.nii.gz: [testng] 13:51:07,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 13:51:07,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:51:07,962 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-06_13-51-07.log] [testng] 13:51:07,963 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e9e38e5 - End of configuration. [testng] [2024-12-06 13:51:13,474] [pool-1-thread-2] Initializing /data/public/NIH/avg152T1_RL_nifti.nii: [testng] 13:51:13,474 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 13:51:13,474 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:51:13,475 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-06_13-51-13.log] [testng] 13:51:13,475 |-INFO in ch.qos.logback.core.sift.SiftProcessor@648c111e - End of configuration. [testng] [2024-12-06 13:51:19,667] [pool-1-thread-11] Initializing /data/public/NIH/avg152T1_LR_nifti.hdr: [testng] [2024-12-06 13:51:20,299] [pool-1-thread-2] Initializing /data/public/NIH/minimal.nii: [testng] [2024-12-06 13:51:20,860] [pool-1-thread-10] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_27_conf_86.hdr: [testng] [2024-12-06 13:51:22,087] [pool-1-thread-6] Initializing /data/public/NIH/zstat1.nii.gz: [testng] [2024-12-06 13:51:26,775] [pool-1-thread-1] Initializing /data/public/NIH/avg152T1_RL_nifti.nii.gz: [testng] [2024-12-06 13:51:29,454] [pool-1-thread-5] Initializing /data/public/NIH/zstat1.nii: [testng] [2024-12-06 13:51:30,063] [pool-1-thread-12] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_94.hdr: [testng] [2024-12-06 13:51:30,688] [pool-1-thread-4] 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: 2 minutes 1 second Finished: SUCCESS