Started by upstream project "BIOFORMATS-test-repo" build number 61
originally caused by:
Started by upstream project "Trigger" build number 68
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9
[BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins5680723187428675310.sh
+ '[' nrrd = slidebook ']'
++ date +%u
+ '[' 7 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_9104_merge_ci -v /uod/idr/repos/curated/nrrd:/data -v /uod/idr-scratch/merge-ci/curated/nrrd:/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] 02:12:21,717 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 02:12:21,718 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service.
[testng] 02:12:21,718 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:12:21,719 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:12:21,720 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 02:12:21,720 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 02:12:21,721 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 02:12:21,721 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:12:21,721 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:12:21,722 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 02:12:21,722 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 02:12:21,722 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 02:12:21,896 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 02:12:21,897 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 02:12:21,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 02:12:21,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 02:12:21,923 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 02:12:21,923 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 02:12:21,923 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 02:12:21,924 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 02:12:21,924 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration.
[testng] 02:12:21,925 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point
[testng] 02:12:21,925 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 204 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-05-12 02:12:21,936] [main] java.version = 17.0.2
[testng] 02:12:21,939 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 02:12:21,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:12:21,984 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-12_02-12-21.log]
[testng] 02:12:21,985 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration.
[testng] [2024-05-12 02:12:21,987] [main] testng.directory = /data
[testng] [2024-05-12 02:12:21,987] [main] testng.configDirectory = /config
[testng] [2024-05-12 02:12:21,996] [main] testng.multiplier = 1.0
[testng] [2024-05-12 02:12:21,996] [main] testng.in-memory = false
[testng] [2024-05-12 02:12:21,996] [main] testng.allow-missing = false
[testng] [2024-05-12 02:12:21,997] [main] user.language = en
[testng] [2024-05-12 02:12:21,997] [main] user.country = ${user.country}
[testng] [2024-05-12 02:12:21,997] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-05-12 02:14:00,993] [main] ----------------------------------------
[testng] [2024-05-12 02:14:00,993] [main] Total files: 14
[testng] [2024-05-12 02:14:00,993] [main] Scan time: 98.996 s (7071 ms/file)
[testng] [2024-05-12 02:14:00,993] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 10 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-05-12 02:14:01,960] [pool-1-thread-1] Initializing /data/greg/average-goodbrains-warp40-5_e1e-2.PIC.gz.nhdr:
[testng] 02:14:01,960 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:14:01,960 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:14:01,961 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-12_02-14-01.log]
[testng] 02:14:01,962 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41bec90e - End of configuration.
[testng] [2024-05-12 02:14:01,989] [pool-1-thread-10] Initializing /data/public/gordon/gk2-rcc-mask.nhdr:
[testng] 02:14:01,989 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:14:01,989 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:14:01,991 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-12_02-14-01.log]
[testng] 02:14:01,991 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ed65d85 - End of configuration.
[testng] [2024-05-12 02:14:02,009] [pool-1-thread-9] Initializing /data/greg/average-goodbrains-warp40-5_e1e-2.PIC.nhdr:
[testng] 02:14:02,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:14:02,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:14:02,010 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-12_02-14-02.log]
[testng] 02:14:02,010 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3356500e - End of configuration.
[testng] [2024-05-12 02:14:02,025] [pool-1-thread-8] Initializing /data/public/glencoe/gzip/dt-helix.nrrd.gz:
[testng] 02:14:02,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:14:02,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:14:02,026 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-12_02-14-02.log]
[testng] 02:14:02,027 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f39ee79 - End of configuration.
[testng] [2024-05-12 02:14:02,149] [pool-1-thread-7] Initializing /data/public/gordon/gk2-rcc-mask2.nhdr:
[testng] 02:14:02,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:14:02,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:14:02,150 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-12_02-14-02.log]
[testng] 02:14:02,150 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2207a966 - End of configuration.
[testng] [2024-05-12 02:14:02,175] [pool-1-thread-6] Initializing /data/public/gordon/dt-helix.nhdr:
[testng] 02:14:02,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:14:02,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:14:02,176 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-12_02-14-02.log]
[testng] 02:14:02,176 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c59eb6d - End of configuration.
[testng] [2024-05-12 02:14:02,197] [pool-1-thread-5] Initializing /data/public/glencoe/version4/dt-helix.nhdr:
[testng] 02:14:02,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:14:02,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:14:02,198 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-12_02-14-02.log]
[testng] 02:14:02,198 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7348a1a1 - End of configuration.
[testng] [2024-05-12 02:14:02,215] [pool-1-thread-4] Initializing /data/greg/average-goodbrains-warp40-5_e1e-2.am.nrrd:
[testng] 02:14:02,215 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:14:02,215 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:14:02,216 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-12_02-14-02.log]
[testng] 02:14:02,217 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f307cac - End of configuration.
[testng] [2024-05-12 02:14:02,320] [pool-1-thread-3] Initializing /data/public/midas/01011-dwi.nhdr:
[testng] 02:14:02,320 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:14:02,320 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:14:02,321 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-12_02-14-02.log]
[testng] 02:14:02,322 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3aa073d - End of configuration.
[testng] [2024-05-12 02:14:02,349] [pool-1-thread-2] Initializing /data/carlos/big4DImage.nrrd:
[testng] 02:14:02,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:14:02,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:14:02,350 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-12_02-14-02.log]
[testng] 02:14:02,351 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d51cc2a - End of configuration.
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 530, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 3 minutes 28 seconds
Finished: SUCCESS