Started by upstream project "BIOFORMATS-test-repo" build number 36
originally caused by:
Started by upstream project "Trigger" build number 40
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7
[BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins6485479194699007452.sh
+ '[' nifti = slidebook ']'
++ date +%u
+ '[' 2 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_5041_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
[javac] warning: [options] bootstrap class path not set in conjunction with -source 8
[javac] 1 warning
test-automated:
[testng] WARNING: An illegal reflective access operation has occurred
[testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket
[testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener
[testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
[testng] WARNING: All illegal access operations will be denied in a future release
[testng] File leak detector installed
[testng] 02:33:32,077 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 02:33:32,079 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service.
[testng] 02:33:32,079 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:33:32,080 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:33:32,080 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 02:33:32,080 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 02:33:32,081 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 02:33:32,081 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:33:32,081 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:33:32,082 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 02:33:32,082 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 02:33:32,083 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 02:33:32,261 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 02:33:32,261 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 02:33:32,286 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 02:33:32,286 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 02:33:32,291 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 02:33:32,292 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 02:33:32,292 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 02:33:32,292 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 02:33:32,292 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration.
[testng] 02:33:32,293 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point
[testng] 02:33:32,293 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 212 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-04-16 02:33:32,303] [main] java.version = 11.0.16
[testng] 02:33:32,306 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 02:33:32,306 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:33:32,351 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-16_02-33-32.log]
[testng] 02:33:32,352 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
[testng] [2024-04-16 02:33:32,354] [main] testng.directory = /data
[testng] [2024-04-16 02:33:32,354] [main] testng.configDirectory = /config
[testng] [2024-04-16 02:33:32,364] [main] testng.multiplier = 1.0
[testng] [2024-04-16 02:33:32,366] [main] testng.in-memory = false
[testng] [2024-04-16 02:33:32,366] [main] testng.allow-missing = false
[testng] [2024-04-16 02:33:32,366] [main] user.language = en
[testng] [2024-04-16 02:33:32,366] [main] user.country = ${user.country}
[testng] [2024-04-16 02:33:32,366] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-04-16 02:33:33,165] [main] ----------------------------------------
[testng] [2024-04-16 02:33:33,165] [main] Total files: 23
[testng] [2024-04-16 02:33:33,165] [main] Scan time: 0.799 s (34 ms/file)
[testng] [2024-04-16 02:33:33,165] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 20 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-04-16 02:33:37,672] [pool-1-thread-1] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_26_conf_91.hdr:
[testng] 02:33:37,673 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:33:37,673 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:33:37,675 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-16_02-33-37.log]
[testng] 02:33:37,675 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f41d2bf - End of configuration.
[testng] [2024-04-16 02:33:37,697] [pool-1-thread-12] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_94.hdr:
[testng] 02:33:37,697 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:33:37,697 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:33:37,699 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-16_02-33-37.log]
[testng] 02:33:37,699 |-INFO in ch.qos.logback.core.sift.SiftProcessor@182319d1 - End of configuration.
[testng] [2024-04-16 02:33:37,718] [pool-1-thread-11] Initializing /data/qa-17334/volume4d.nii:
[testng] 02:33:37,718 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:33:37,718 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:33:37,719 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-16_02-33-37.log]
[testng] 02:33:37,719 |-INFO in ch.qos.logback.core.sift.SiftProcessor@538adf4a - End of configuration.
[testng] [2024-04-16 02:33:37,743] [pool-1-thread-10] Initializing /data/public/NIH/newsirp_final_XML.nii:
[testng] 02:33:37,743 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:33:37,743 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:33:37,744 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-16_02-33-37.log]
[testng] 02:33:37,744 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49e6004b - End of configuration.
[testng] [2024-04-16 02:33:37,767] [pool-1-thread-9] Initializing /data/public/NIH/avg152T1_LR_nifti.nii.gz:
[testng] 02:33:37,767 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:33:37,767 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:33:37,767 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-16_02-33-37.log]
[testng] 02:33:37,768 |-INFO in ch.qos.logback.core.sift.SiftProcessor@de2d619 - End of configuration.
[testng] [2024-04-16 02:33:37,954] [pool-1-thread-8] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_100.hdr:
[testng] 02:33:37,954 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:33:37,954 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:33:37,955 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-16_02-33-37.log]
[testng] 02:33:37,955 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d178726 - End of configuration.
[testng] [2024-04-16 02:33:37,968] [pool-1-thread-7] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_27_conf_86.hdr:
[testng] 02:33:37,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:33:37,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:33:37,968 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-16_02-33-37.log]
[testng] 02:33:37,969 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53857774 - End of configuration.
[testng] [2024-04-16 02:33:37,981] [pool-1-thread-6] Initializing /data/public/NIH/avg152T1_RL_nifti.nii.gz:
[testng] 02:33:37,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:33:37,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:33:37,982 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-16_02-33-37.log]
[testng] 02:33:37,983 |-INFO in ch.qos.logback.core.sift.SiftProcessor@163b808a - End of configuration.
[testng] [2024-04-16 02:33:38,164] [pool-1-thread-5] Initializing /data/public/NIH/minimal.hdr:
[testng] 02:33:38,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:33:38,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:33:38,164 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-16_02-33-38.log]
[testng] 02:33:38,165 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7dc69d2c - End of configuration.
[testng] [2024-04-16 02:33:38,174] [pool-1-thread-4] Initializing /data/public/NIH/avg152T1_RL_nifti.nii:
[testng] 02:33:38,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:33:38,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:33:38,175 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-16_02-33-38.log]
[testng] 02:33:38,175 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37081102 - End of configuration.
[testng] [2024-04-16 02:33:38,196] [pool-1-thread-3] Initializing /data/public/NIH/avg152T1_LR_nifti.nii:
[testng] 02:33:38,196 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:33:38,196 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:33:38,197 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-16_02-33-38.log]
[testng] 02:33:38,198 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35f8d2ee - End of configuration.
[testng] [2024-04-16 02:33:38,235] [pool-1-thread-2] Initializing /data/public/NIH/zstat1.nii:
[testng] 02:33:38,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:33:38,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:33:38,236 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-16_02-33-38.log]
[testng] 02:33:38,237 |-INFO in ch.qos.logback.core.sift.SiftProcessor@188edbbf - End of configuration.
[testng] [2024-04-16 02:33:39,791] [pool-1-thread-11] Initializing /data/public/NIH/avg152T1_LR_nifti.hdr:
[testng] [2024-04-16 02:33:39,804] [pool-1-thread-4] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_100.hdr:
[testng] [2024-04-16 02:33:39,820] [pool-1-thread-2] Initializing /data/public/NIH/minimal.nii:
[testng] [2024-04-16 02:33:39,834] [pool-1-thread-12] Initializing /data/public/NIH/avg152T1_RL_nifti.hdr:
[testng] [2024-04-16 02:33:39,844] [pool-1-thread-1] Initializing /data/public/NIH/zstat1.nii.gz:
[testng] [2024-04-16 02:33:39,904] [pool-1-thread-8] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_94.hdr:
[testng] [2024-04-16 02:33:39,913] [pool-1-thread-7] Initializing /data/public/NIH/filtered_func_data.nii:
[testng] [2024-04-16 02:33:39,942] [pool-1-thread-10] Initializing /data/public/NIH/filtered_func_data.nii.gz:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1060, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 39 seconds
Finished: SUCCESS