Started by upstream project "BIOFORMATS-test-repo" build number 273 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins2359707210899555461.sh + '[' nifti = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_43108_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] 12:19:08,647 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 12:19:08,649 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 12:19:08,649 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:19:08,650 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:19:08,650 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 12:19:08,650 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 12:19:08,650 |-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] 12:19:08,650 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:19:08,651 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:19:08,651 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 12:19:08,651 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 12:19:08,651 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 12:19:08,860 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 12:19:08,860 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 12:19:08,886 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 12:19:08,886 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 12:19:08,893 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 12:19:08,894 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 12:19:08,894 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 12:19:08,894 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 12:19:08,894 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 12:19:08,895 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 12:19:08,895 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 244 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-29 12:19:08,904] [main] java.version = 1.8.0_342 [testng] 12:19:08,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 12:19:08,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:19:08,950 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-29_12-19-08.log] [testng] 12:19:08,951 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-29 12:19:08,953] [main] testng.directory = /data [testng] [2024-11-29 12:19:08,953] [main] testng.configDirectory = /config [testng] [2024-11-29 12:19:08,964] [main] testng.multiplier = 1.0 [testng] [2024-11-29 12:19:08,964] [main] testng.in-memory = false [testng] [2024-11-29 12:19:08,964] [main] testng.allow-missing = false [testng] [2024-11-29 12:19:08,965] [main] user.language = en [testng] [2024-11-29 12:19:08,965] [main] user.country = ${user.country} [testng] [2024-11-29 12:19:08,965] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-29 12:19:25,009] [main] ---------------------------------------- [testng] [2024-11-29 12:19:25,009] [main] Total files: 23 [testng] [2024-11-29 12:19:25,009] [main] Scan time: 16.044 s (697 ms/file) [testng] [2024-11-29 12:19:25,009] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-29 12:20:05,494] [pool-1-thread-1] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_26_conf_91.hdr: [testng] 12:20:05,494 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 12:20:05,494 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:20:05,495 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-29_12-20-05.log] [testng] 12:20:05,496 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68d01a35 - End of configuration. [testng] [2024-11-29 12:20:06,403] [pool-1-thread-12] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_100.hdr: [testng] 12:20:06,404 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 12:20:06,404 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:20:06,405 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-29_12-20-06.log] [testng] 12:20:06,405 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3716adc8 - End of configuration. [testng] [2024-11-29 12:20:07,279] [pool-1-thread-11] Initializing /data/qa-17334/volume4d.nii: [testng] 12:20:07,279 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 12:20:07,279 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:20:07,280 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-29_12-20-07.log] [testng] 12:20:07,280 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9ea5c19 - End of configuration. [testng] [2024-11-29 12:20:08,141] [pool-1-thread-10] Initializing /data/public/NIH/filtered_func_data.nii: [testng] 12:20:08,141 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 12:20:08,141 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:20:08,141 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-29_12-20-08.log] [testng] 12:20:08,142 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56a8ce36 - End of configuration. [testng] [2024-11-29 12:20:09,026] [pool-1-thread-9] Initializing /data/public/NIH/avg152T1_LR_nifti.nii.gz: [testng] 12:20:09,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 12:20:09,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:20:09,026 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-29_12-20-09.log] [testng] 12:20:09,027 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d2e6e16 - End of configuration. [testng] [2024-11-29 12:20:12,732] [pool-1-thread-8] Initializing /data/public/NIH/minimal.hdr: [testng] 12:20:12,733 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 12:20:12,733 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:20:12,733 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-29_12-20-12.log] [testng] 12:20:12,734 |-INFO in ch.qos.logback.core.sift.SiftProcessor@315d0ae6 - End of configuration. [testng] [2024-11-29 12:20:13,603] [pool-1-thread-7] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_100.hdr: [testng] 12:20:13,604 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 12:20:13,604 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:20:13,604 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-29_12-20-13.log] [testng] 12:20:13,605 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d3e93a8 - End of configuration. [testng] [2024-11-29 12:20:14,461] [pool-1-thread-6] Initializing /data/public/NIH/newsirp_final_XML.nii: [testng] 12:20:14,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 12:20:14,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:20:14,462 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-29_12-20-14.log] [testng] 12:20:14,462 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32061fd7 - End of configuration. [testng] [2024-11-29 12:20:15,314] [pool-1-thread-5] Initializing /data/public/NIH/avg152T1_RL_nifti.hdr: [testng] 12:20:15,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 12:20:15,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:20:15,315 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-29_12-20-15.log] [testng] 12:20:15,315 |-INFO in ch.qos.logback.core.sift.SiftProcessor@500653ad - End of configuration. [testng] [2024-11-29 12:20:16,307] [pool-1-thread-4] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_94.hdr: [testng] 12:20:16,307 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 12:20:16,307 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:20:16,308 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-29_12-20-16.log] [testng] 12:20:16,308 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a5ac41d - End of configuration. [testng] [2024-11-29 12:20:17,297] [pool-1-thread-3] Initializing /data/public/NIH/filtered_func_data.nii.gz: [testng] 12:20:17,297 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 12:20:17,297 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:20:17,298 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-29_12-20-17.log] [testng] 12:20:17,298 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68c2b028 - End of configuration. [testng] [2024-11-29 12:20:23,900] [pool-1-thread-2] Initializing /data/public/NIH/avg152T1_RL_nifti.nii: [testng] 12:20:23,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 12:20:23,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:20:23,902 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-29_12-20-23.log] [testng] 12:20:23,902 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a0e2326 - End of configuration. [testng] [2024-11-29 12:20:32,738] [pool-1-thread-11] Initializing /data/public/NIH/avg152T1_LR_nifti.hdr: [testng] [2024-11-29 12:20:33,760] [pool-1-thread-2] Initializing /data/public/NIH/minimal.nii: [testng] [2024-11-29 12:20:34,835] [pool-1-thread-6] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_27_conf_86.hdr: [testng] [2024-11-29 12:20:35,926] [pool-1-thread-10] Initializing /data/public/NIH/zstat1.nii.gz: [testng] [2024-11-29 12:20:41,562] [pool-1-thread-12] Initializing /data/public/NIH/avg152T1_RL_nifti.nii.gz: [testng] [2024-11-29 12:20:45,917] [pool-1-thread-8] Initializing /data/public/NIH/zstat1.nii: [testng] [2024-11-29 12:20:46,947] [pool-1-thread-5] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_94.hdr: [testng] [2024-11-29 12:20:47,935] [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 20 seconds Finished: SUCCESS