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Started by upstream project "BIOFORMATS-test-repo" build number 112 originally caused by: Started by upstream project "Trigger" build number 125 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins2280215154200500117.sh + '[' nifti = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_17506_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] 02:46:30,114 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:46:30,117 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 02:46:30,117 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:46:30,119 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:46:30,119 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:46:30,119 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:46:30,120 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:46:30,120 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:46:30,120 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:46:30,121 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:46:30,121 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:46:30,121 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:46:30,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:46:30,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:46:30,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:46:30,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:46:30,442 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:46:30,442 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:46:30,443 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:46:30,443 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:46:30,443 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 02:46:30,444 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 02:46:30,444 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 324 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-05 02:46:30,455] [main] java.version = 1.8.0_342 [testng] 02:46:30,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:46:30,460 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:30,509 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-05_02-46-30.log] [testng] 02:46:30,514 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-07-05 02:46:30,517] [main] testng.directory = /data [testng] [2024-07-05 02:46:30,517] [main] testng.configDirectory = /config [testng] [2024-07-05 02:46:30,531] [main] testng.multiplier = 1.0 [testng] [2024-07-05 02:46:30,531] [main] testng.in-memory = false [testng] [2024-07-05 02:46:30,531] [main] testng.allow-missing = false [testng] [2024-07-05 02:46:30,531] [main] user.language = en [testng] [2024-07-05 02:46:30,531] [main] user.country = ${user.country} [testng] [2024-07-05 02:46:30,531] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-07-05 02:46:31,378] [main] ---------------------------------------- [testng] [2024-07-05 02:46:31,378] [main] Total files: 23 [testng] [2024-07-05 02:46:31,378] [main] Scan time: 0.846 s (36 ms/file) [testng] [2024-07-05 02:46:31,378] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-05 02:46:36,317] [pool-1-thread-1] Initializing /data/public/NIH/filtered_func_data.nii.gz: [testng] 02:46:36,318 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:46:36,318 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:36,318 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-05_02-46-36.log] [testng] 02:46:36,319 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ee16b44 - End of configuration. [testng] [2024-07-05 02:46:39,490] [pool-1-thread-12] Initializing /data/public/NIH/minimal.nii: [testng] 02:46:39,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:46:39,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:39,491 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-05_02-46-39.log] [testng] 02:46:39,491 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79f11383 - End of configuration. [testng] [2024-07-05 02:46:39,502] [pool-1-thread-11] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_94.hdr: [testng] 02:46:39,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:46:39,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:39,502 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-05_02-46-39.log] [testng] 02:46:39,503 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d4ee600 - End of configuration. [testng] [2024-07-05 02:46:39,513] [pool-1-thread-10] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_100.hdr: [testng] 02:46:39,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:46:39,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:39,514 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-05_02-46-39.log] [testng] 02:46:39,514 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f2b7732 - End of configuration. [testng] [2024-07-05 02:46:39,526] [pool-1-thread-9] Initializing /data/qa-17334/volume4d.nii: [testng] 02:46:39,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:46:39,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:39,526 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-05_02-46-39.log] [testng] 02:46:39,527 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c4e4bee - End of configuration. [testng] [2024-07-05 02:46:39,549] [pool-1-thread-8] Initializing /data/public/NIH/avg152T1_RL_nifti.nii.gz: [testng] 02:46:39,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:46:39,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:39,550 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-05_02-46-39.log] [testng] 02:46:39,550 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c43ef25 - End of configuration. [testng] [2024-07-05 02:46:39,769] [pool-1-thread-7] Initializing /data/public/NIH/avg152T1_LR_nifti.nii.gz: [testng] 02:46:39,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:46:39,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:39,770 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-05_02-46-39.log] [testng] 02:46:39,770 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d80dd3 - End of configuration. [testng] [2024-07-05 02:46:40,009] [pool-1-thread-6] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_94.hdr: [testng] 02:46:40,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:46:40,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:40,010 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-05_02-46-40.log] [testng] 02:46:40,010 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3baa194d - End of configuration. [testng] [2024-07-05 02:46:40,022] [pool-1-thread-5] Initializing /data/public/NIH/filtered_func_data.nii: [testng] 02:46:40,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:46:40,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:40,023 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-05_02-46-40.log] [testng] 02:46:40,023 |-INFO in ch.qos.logback.core.sift.SiftProcessor@507af7f8 - End of configuration. [testng] [2024-07-05 02:46:40,046] [pool-1-thread-4] Initializing /data/public/NIH/avg152T1_LR_nifti.nii: [testng] 02:46:40,047 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:46:40,047 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:40,047 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-05_02-46-40.log] [testng] 02:46:40,048 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ef00d08 - End of configuration. [testng] [2024-07-05 02:46:40,068] [pool-1-thread-3] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_100.hdr: [testng] 02:46:40,069 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:46:40,069 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:40,070 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-05_02-46-40.log] [testng] 02:46:40,070 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62150b7f - End of configuration. [testng] [2024-07-05 02:46:40,085] [pool-1-thread-2] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_27_conf_86.hdr: [testng] 02:46:40,086 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:46:40,086 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:40,087 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-05_02-46-40.log] [testng] 02:46:40,088 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b975c30 - End of configuration. [testng] [2024-07-05 02:46:41,315] [pool-1-thread-12] Initializing /data/public/NIH/zstat1.nii: [testng] [2024-07-05 02:46:41,330] [pool-1-thread-6] Initializing /data/public/NIH/newsirp_final_XML.nii: [testng] [2024-07-05 02:46:41,348] [pool-1-thread-11] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_26_conf_91.hdr: [testng] [2024-07-05 02:46:41,357] [pool-1-thread-2] Initializing /data/public/NIH/zstat1.nii.gz: [testng] [2024-07-05 02:46:41,442] [pool-1-thread-3] Initializing /data/public/NIH/avg152T1_LR_nifti.hdr: [testng] [2024-07-05 02:46:41,452] [pool-1-thread-10] Initializing /data/public/NIH/avg152T1_RL_nifti.hdr: [testng] [2024-07-05 02:46:41,466] [pool-1-thread-9] Initializing /data/public/NIH/minimal.hdr: [testng] [2024-07-05 02:46:41,477] [pool-1-thread-5] Initializing /data/public/NIH/avg152T1_RL_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: 44 seconds Finished: SUCCESS