Started by upstream project "BIOFORMATS-test-repo" build number 106
originally caused by:
Started by upstream project "Trigger" build number 118
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4
[BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins12276125742246933571.sh
+ '[' minc = slidebook ']'
++ date +%u
+ '[' 6 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_16445_merge_ci -v /uod/idr/repos/curated/minc:/data -v /uod/idr-scratch/merge-ci/curated/minc:/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] 01:47:41,980 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:47:41,981 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service.
[testng] 01:47:41,981 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:47:41,982 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:47:41,983 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:47:41,983 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:47:41,984 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:47:41,984 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:47:41,984 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:47:41,985 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:47:41,985 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:47:41,986 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:47:42,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:47:42,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:47:42,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:47:42,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:47:42,187 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:47:42,187 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:47:42,188 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:47:42,188 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:47:42,188 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration.
[testng] 01:47:42,189 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point
[testng] 01:47:42,189 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 205 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-06-29 01:47:42,199] [main] java.version = 11.0.16
[testng] 01:47:42,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:47:42,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:47:42,251 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-29_01-47-42.log]
[testng] 01:47:42,253 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
[testng] [2024-06-29 01:47:42,255] [main] testng.directory = /data
[testng] [2024-06-29 01:47:42,255] [main] testng.configDirectory = /config
[testng] [2024-06-29 01:47:42,266] [main] testng.multiplier = 1.0
[testng] [2024-06-29 01:47:42,267] [main] testng.in-memory = false
[testng] [2024-06-29 01:47:42,267] [main] testng.allow-missing = false
[testng] [2024-06-29 01:47:42,267] [main] user.language = en
[testng] [2024-06-29 01:47:42,267] [main] user.country = ${user.country}
[testng] [2024-06-29 01:47:42,267] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-06-29 01:47:42,670] [main] ----------------------------------------
[testng] [2024-06-29 01:47:42,670] [main] Total files: 15
[testng] [2024-06-29 01:47:42,671] [main] Scan time: 0.402 s (26 ms/file)
[testng] [2024-06-29 01:47:42,671] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 15 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-06-29 01:47:50,378] [pool-1-thread-1] Initializing /data/samples/ICBM/icbm_template_2.00mm.mnc:
[testng] 01:47:50,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:47:50,379 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:47:50,381 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-29_01-47-50.log]
[testng] 01:47:50,381 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d7fa90f - End of configuration.
[testng] [2024-06-29 01:47:50,407] [pool-1-thread-12] Initializing /data/bigbrain/full16_400um_2009b_sym.mnc:
[testng] 01:47:50,407 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:47:50,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:47:50,409 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-29_01-47-50.log]
[testng] 01:47:50,409 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c9dbed2 - End of configuration.
[testng] [2024-06-29 01:47:52,889] [pool-1-thread-11] Initializing /data/samples/ICBM/icbm_template_zero.75mm.mnc:
[testng] 01:47:52,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:47:52,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:47:52,891 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-29_01-47-52.log]
[testng] 01:47:52,892 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42c7d191 - End of configuration.
[testng] [2024-06-29 01:47:52,957] [pool-1-thread-10] Initializing /data/samples/ICBM/icbm_template_zero.50mm.mnc:
[testng] 01:47:52,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:47:52,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:47:52,960 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-29_01-47-52.log]
[testng] 01:47:52,961 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53eb92b1 - End of configuration.
[testng] [2024-06-29 01:47:53,318] [pool-1-thread-9] Initializing /data/samples/ICBM/icbm_template_6.00mm.mnc:
[testng] 01:47:53,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:47:53,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:47:53,319 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-29_01-47-53.log]
[testng] 01:47:53,320 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ecbaa54 - End of configuration.
[testng] [2024-06-29 01:47:53,330] [pool-1-thread-8] Initializing /data/samples/ICBM/icbm_atlas_cerebellum_avg_53_mask_1mm.mnc:
[testng] 01:47:53,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:47:53,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:47:53,330 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-29_01-47-53.log]
[testng] 01:47:53,331 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76e717aa - End of configuration.
[testng] [2024-06-29 01:47:53,362] [pool-1-thread-7] Initializing /data/bigbrain/pm6479o.mnc:
[testng] 01:47:53,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:47:53,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:47:53,363 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-29_01-47-53.log]
[testng] 01:47:53,364 |-INFO in ch.qos.logback.core.sift.SiftProcessor@611746ba - End of configuration.
[testng] [2024-06-29 01:47:54,007] [pool-1-thread-6] Initializing /data/samples/ICBM/icbm_template_one.50mm.mnc:
[testng] 01:47:54,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:47:54,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:47:54,008 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-29_01-47-54.log]
[testng] 01:47:54,009 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8b3bc7f - End of configuration.
[testng] [2024-06-29 01:47:54,022] [pool-1-thread-5] Initializing /data/samples/ICBM/icbm_template_one.00mm.mnc:
[testng] 01:47:54,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:47:54,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:47:54,023 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-29_01-47-54.log]
[testng] 01:47:54,023 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14c7ad0d - End of configuration.
[testng] [2024-06-29 01:47:54,045] [pool-1-thread-4] Initializing /data/samples/ICBM/icbm_template_3.00mm.mnc:
[testng] 01:47:54,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:47:54,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:47:54,046 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-29_01-47-54.log]
[testng] 01:47:54,047 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4fecb5b6 - End of configuration.
[testng] [2024-06-29 01:47:54,057] [pool-1-thread-3] Initializing /data/bigbrain/8-bit_full_400um_2009b_sym.mnc:
[testng] 01:47:54,058 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:47:54,058 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:47:54,058 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-29_01-47-54.log]
[testng] 01:47:54,058 |-INFO in ch.qos.logback.core.sift.SiftProcessor@180b897a - End of configuration.
[testng] [2024-06-29 01:47:54,990] [pool-1-thread-2] Initializing /data/samples/ICBM/icbm_template_4.00mm.mnc:
[testng] 01:47:54,990 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:47:54,990 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:47:54,991 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-29_01-47-54.log]
[testng] 01:47:54,991 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5569619d - End of configuration.
BUILD SUCCESSFUL
Total time: 32 seconds
Finished: SUCCESS