Started by upstream project "BIOFORMATS-test-repo" build number 79
originally caused by:
Started by upstream project "Trigger" build number 87
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder
[BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins3186145360927458630.sh
+ '[' nifti = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_12094_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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release
[javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
[javac] 4 warnings
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] 02:40:10,506 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 02:40:10,507 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service.
[testng] 02:40:10,507 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:40:10,508 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:40:10,508 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 02:40:10,508 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 02:40:10,509 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 02:40:10,509 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:40:10,509 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:40:10,510 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 02:40:10,510 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 02:40:10,510 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 02:40:10,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 02:40:10,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 02:40:10,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 02:40:10,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 02:40:10,693 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 02:40:10,694 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 02:40:10,694 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 02:40:10,694 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 02:40:10,694 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration.
[testng] 02:40:10,695 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point
[testng] 02:40:10,695 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 186 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-05-30 02:40:10,703] [main] java.version = 21
[testng] 02:40:10,707 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 02:40:10,707 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:40:10,753 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-30_02-40-10.log]
[testng] 02:40:10,755 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration.
[testng] [2024-05-30 02:40:10,757] [main] testng.directory = /data
[testng] [2024-05-30 02:40:10,757] [main] testng.configDirectory = /config
[testng] [2024-05-30 02:40:10,770] [main] testng.multiplier = 1.0
[testng] [2024-05-30 02:40:10,771] [main] testng.in-memory = false
[testng] [2024-05-30 02:40:10,771] [main] testng.allow-missing = false
[testng] [2024-05-30 02:40:10,771] [main] user.language = en
[testng] [2024-05-30 02:40:10,771] [main] user.country = ${user.country}
[testng] [2024-05-30 02:40:10,771] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-05-30 02:40:11,643] [main] ----------------------------------------
[testng] [2024-05-30 02:40:11,643] [main] Total files: 23
[testng] [2024-05-30 02:40:11,643] [main] Scan time: 0.872 s (37 ms/file)
[testng] [2024-05-30 02:40:11,643] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 20 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-05-30 02:40:16,220] [pool-1-thread-1] Initializing /data/public/NIH/avg152T1_LR_nifti.hdr:
[testng] 02:40:16,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:40:16,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:40:16,222 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-30_02-40-16.log]
[testng] 02:40:16,223 |-INFO in ch.qos.logback.core.sift.SiftProcessor@391fc928 - End of configuration.
[testng] [2024-05-30 02:40:16,242] [pool-1-thread-12] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_27_conf_86.hdr:
[testng] 02:40:16,243 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:40:16,243 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:40:16,244 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-30_02-40-16.log]
[testng] 02:40:16,244 |-INFO in ch.qos.logback.core.sift.SiftProcessor@249dcb20 - End of configuration.
[testng] [2024-05-30 02:40:16,266] [pool-1-thread-11] Initializing /data/qa-17334/volume4d.nii:
[testng] 02:40:16,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:40:16,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:40:16,267 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-30_02-40-16.log]
[testng] 02:40:16,268 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10ee589 - End of configuration.
[testng] [2024-05-30 02:40:16,299] [pool-1-thread-10] Initializing /data/public/NIH/avg152T1_LR_nifti.nii.gz:
[testng] 02:40:16,300 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:40:16,300 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:40:16,300 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-30_02-40-16.log]
[testng] 02:40:16,301 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e724045 - End of configuration.
[testng] [2024-05-30 02:40:16,572] [pool-1-thread-9] Initializing /data/public/NIH/newsirp_final_XML.nii:
[testng] 02:40:16,572 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:40:16,572 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:40:16,573 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-30_02-40-16.log]
[testng] 02:40:16,573 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33298cd8 - End of configuration.
[testng] [2024-05-30 02:40:16,591] [pool-1-thread-8] Initializing /data/public/NIH/minimal.nii:
[testng] 02:40:16,591 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:40:16,591 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:40:16,592 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-30_02-40-16.log]
[testng] 02:40:16,593 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7eec7a4b - End of configuration.
[testng] [2024-05-30 02:40:16,606] [pool-1-thread-7] Initializing /data/public/NIH/avg152T1_RL_nifti.hdr:
[testng] 02:40:16,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:40:16,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:40:16,615 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-30_02-40-16.log]
[testng] 02:40:16,616 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b0c5afb - End of configuration.
[testng] [2024-05-30 02:40:16,630] [pool-1-thread-6] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_26_conf_91.hdr:
[testng] 02:40:16,630 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:40:16,630 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:40:16,631 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-30_02-40-16.log]
[testng] 02:40:16,631 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2147e37e - End of configuration.
[testng] [2024-05-30 02:40:16,644] [pool-1-thread-5] Initializing /data/public/NIH/zstat1.nii:
[testng] 02:40:16,644 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:40:16,644 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:40:16,645 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-30_02-40-16.log]
[testng] 02:40:16,646 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d39b66d - End of configuration.
[testng] [2024-05-30 02:40:16,660] [pool-1-thread-4] Initializing /data/public/NIH/filtered_func_data.nii.gz:
[testng] 02:40:16,661 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:40:16,661 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:40:16,661 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-30_02-40-16.log]
[testng] 02:40:16,662 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35ce9a97 - End of configuration.
[testng] [2024-05-30 02:40:19,434] [pool-1-thread-3] Initializing /data/public/NIH/filtered_func_data.nii:
[testng] 02:40:19,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:40:19,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:40:19,436 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-30_02-40-19.log]
[testng] 02:40:19,436 |-INFO in ch.qos.logback.core.sift.SiftProcessor@516639ac - End of configuration.
[testng] [2024-05-30 02:40:19,454] [pool-1-thread-2] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_94.hdr:
[testng] 02:40:19,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:40:19,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:40:19,455 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-30_02-40-19.log]
[testng] 02:40:19,456 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7239982c - End of configuration.
[testng] [2024-05-30 02:40:20,889] [pool-1-thread-8] Initializing /data/public/NIH/avg152T1_LR_nifti.nii:
[testng] [2024-05-30 02:40:20,908] [pool-1-thread-1] Initializing /data/public/NIH/avg152T1_RL_nifti.nii:
[testng] [2024-05-30 02:40:20,939] [pool-1-thread-3] Initializing /data/public/NIH/avg152T1_RL_nifti.nii.gz:
[testng] [2024-05-30 02:40:21,143] [pool-1-thread-2] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_100.hdr:
[testng] [2024-05-30 02:40:21,157] [pool-1-thread-9] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_100.hdr:
[testng] [2024-05-30 02:40:21,168] [pool-1-thread-12] Initializing /data/public/NIH/zstat1.nii.gz:
[testng] [2024-05-30 02:40:21,228] [pool-1-thread-6] Initializing /data/public/NIH/minimal.hdr:
[testng] [2024-05-30 02:40:21,237] [pool-1-thread-11] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_94.hdr:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1060, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 40 seconds
Finished: SUCCESS