Started by upstream project "BIOFORMATS-test-repo" build number 287
originally caused by:
Started by upstream project "Trigger" build number 306
originally caused by:
Started by timer
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/jenkins11865128190713525550.sh
+ '[' nifti = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_45406_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] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket
[testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket
[testng] File leak detector installed
[testng] 06:12:20,059 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 06:12:20,060 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service.
[testng] 06:12:20,060 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 06:12:20,061 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 06:12:20,062 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 06:12:20,062 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 06:12:20,062 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 06:12:20,062 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 06:12:20,063 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 06:12:20,063 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 06:12:20,063 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 06:12:20,064 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 06:12:20,215 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 06:12:20,215 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 06:12:20,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 06:12:20,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 06:12:20,242 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 06:12:20,242 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 06:12:20,242 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 06:12:20,242 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 06:12:20,243 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration.
[testng] 06:12:20,243 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point
[testng] 06:12:20,243 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 180 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-12-11 06:12:20,251] [main] java.version = 17.0.2
[testng] 06:12:20,254 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 06:12:20,255 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:12:20,292 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-11_06-12-20.log]
[testng] 06:12:20,294 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration.
[testng] [2024-12-11 06:12:20,295] [main] testng.directory = /data
[testng] [2024-12-11 06:12:20,296] [main] testng.configDirectory = /config
[testng] [2024-12-11 06:12:20,304] [main] testng.multiplier = 1.0
[testng] [2024-12-11 06:12:20,305] [main] testng.in-memory = false
[testng] [2024-12-11 06:12:20,305] [main] testng.allow-missing = false
[testng] [2024-12-11 06:12:20,305] [main] user.language = en
[testng] [2024-12-11 06:12:20,305] [main] user.country = ${user.country}
[testng] [2024-12-11 06:12:20,305] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-12-11 06:12:41,604] [main] ----------------------------------------
[testng] [2024-12-11 06:12:41,604] [main] Total files: 23
[testng] [2024-12-11 06:12:41,604] [main] Scan time: 21.299 s (926 ms/file)
[testng] [2024-12-11 06:12:41,604] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 20 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-12-11 06:13:38,513] [pool-1-thread-1] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_100.hdr:
[testng] 06:13:38,514 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 06:13:38,514 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:13:38,515 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-11_06-13-38.log]
[testng] 06:13:38,515 |-INFO in ch.qos.logback.core.sift.SiftProcessor@503efc25 - End of configuration.
[testng] [2024-12-11 06:13:39,905] [pool-1-thread-12] Initializing /data/public/NIH/zstat1.nii:
[testng] 06:13:39,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 06:13:39,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:13:39,906 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-11_06-13-39.log]
[testng] 06:13:39,906 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d438e37 - End of configuration.
[testng] [2024-12-11 06:13:41,145] [pool-1-thread-11] Initializing /data/public/NIH/avg152T1_LR_nifti.nii:
[testng] 06:13:41,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 06:13:41,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:13:41,147 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-11_06-13-41.log]
[testng] 06:13:41,147 |-INFO in ch.qos.logback.core.sift.SiftProcessor@380b8202 - End of configuration.
[testng] [2024-12-11 06:13:42,359] [pool-1-thread-10] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_100.hdr:
[testng] 06:13:42,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 06:13:42,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:13:42,360 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-11_06-13-42.log]
[testng] 06:13:42,360 |-INFO in ch.qos.logback.core.sift.SiftProcessor@cc3d36e - End of configuration.
[testng] [2024-12-11 06:13:43,773] [pool-1-thread-9] Initializing /data/public/NIH/zstat1.nii.gz:
[testng] 06:13:43,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 06:13:43,774 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:13:43,774 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-11_06-13-43.log]
[testng] 06:13:43,775 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ad38a0 - End of configuration.
[testng] [2024-12-11 06:13:49,096] [pool-1-thread-8] Initializing /data/public/NIH/avg152T1_LR_nifti.nii.gz:
[testng] 06:13:49,096 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 06:13:49,096 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:13:49,097 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-11_06-13-49.log]
[testng] 06:13:49,097 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20cb239 - End of configuration.
[testng] [2024-12-11 06:13:54,776] [pool-1-thread-7] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_94.hdr:
[testng] 06:13:54,776 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 06:13:54,776 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:13:54,777 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-11_06-13-54.log]
[testng] 06:13:54,777 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b4efa30 - End of configuration.
[testng] [2024-12-11 06:13:56,158] [pool-1-thread-6] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_27_conf_86.hdr:
[testng] 06:13:56,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 06:13:56,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:13:56,159 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-11_06-13-56.log]
[testng] 06:13:56,159 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a67480f - End of configuration.
[testng] [2024-12-11 06:13:57,500] [pool-1-thread-5] Initializing /data/public/NIH/filtered_func_data.nii:
[testng] 06:13:57,500 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 06:13:57,500 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:13:57,501 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-11_06-13-57.log]
[testng] 06:13:57,501 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c8f6f59 - End of configuration.
[testng] [2024-12-11 06:13:58,700] [pool-1-thread-4] Initializing /data/public/NIH/avg152T1_RL_nifti.nii:
[testng] 06:13:58,700 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 06:13:58,700 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:13:58,701 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-11_06-13-58.log]
[testng] 06:13:58,701 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36451b94 - End of configuration.
[testng] [2024-12-11 06:13:59,981] [pool-1-thread-3] Initializing /data/public/NIH/avg152T1_RL_nifti.hdr:
[testng] 06:13:59,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 06:13:59,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:13:59,982 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-11_06-13-59.log]
[testng] 06:13:59,982 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52cbcc5b - End of configuration.
[testng] [2024-12-11 06:14:01,347] [pool-1-thread-2] Initializing /data/public/NIH/newsirp_final_XML.nii:
[testng] 06:14:01,347 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 06:14:01,348 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:14:01,348 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-11_06-14-01.log]
[testng] 06:14:01,348 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56b43735 - End of configuration.
[testng] [2024-12-11 06:14:12,662] [pool-1-thread-11] Initializing /data/public/NIH/filtered_func_data.nii.gz:
[testng] [2024-12-11 06:14:20,368] [pool-1-thread-12] Initializing /data/public/NIH/avg152T1_RL_nifti.nii.gz:
[testng] [2024-12-11 06:14:25,878] [pool-1-thread-4] Initializing /data/public/NIH/minimal.nii:
[testng] [2024-12-11 06:14:27,064] [pool-1-thread-5] Initializing /data/public/NIH/avg152T1_LR_nifti.hdr:
[testng] [2024-12-11 06:14:28,445] [pool-1-thread-2] Initializing /data/qa-17334/volume4d.nii:
[testng] [2024-12-11 06:14:33,529] [pool-1-thread-1] Initializing /data/public/NIH/minimal.hdr:
[testng] [2024-12-11 06:14:34,869] [pool-1-thread-10] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_94.hdr:
[testng] [2024-12-11 06:14:36,221] [pool-1-thread-7] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_26_conf_91.hdr:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1060, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 3 minutes 12 seconds
Finished: SUCCESS