Started by upstream project "BIOFORMATS-test-repo" build number 214
originally caused by:
Started by upstream project "Trigger" build number 241
originally caused by:
Started by user devspace
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/jenkins16212228829174465238.sh
+ '[' minc = slidebook ']'
++ date +%u
+ '[' 2 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_34000_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] 10:06:28,883 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 10:06:28,884 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service.
[testng] 10:06:28,884 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 10:06:28,885 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 10:06:28,886 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 10:06:28,886 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 10:06:28,886 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 10:06:28,886 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 10:06:28,887 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 10:06:28,888 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 10:06:28,888 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 10:06:28,888 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 10:06:29,056 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 10:06:29,056 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 10:06:29,078 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 10:06:29,078 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 10:06:29,084 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 10:06:29,084 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 10:06:29,084 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 10:06:29,084 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 10:06:29,084 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration.
[testng] 10:06:29,085 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point
[testng] 10:06:29,085 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 198 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-10-08 10:06:29,094] [main] java.version = 11.0.16
[testng] 10:06:29,097 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 10:06:29,097 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:06:29,138 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-08_10-06-29.log]
[testng] 10:06:29,140 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration.
[testng] [2024-10-08 10:06:29,143] [main] testng.directory = /data
[testng] [2024-10-08 10:06:29,144] [main] testng.configDirectory = /config
[testng] [2024-10-08 10:06:29,156] [main] testng.multiplier = 1.0
[testng] [2024-10-08 10:06:29,158] [main] testng.in-memory = false
[testng] [2024-10-08 10:06:29,158] [main] testng.allow-missing = false
[testng] [2024-10-08 10:06:29,158] [main] user.language = en
[testng] [2024-10-08 10:06:29,158] [main] user.country = ${user.country}
[testng] [2024-10-08 10:06:29,158] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-10-08 10:06:30,147] [main] ----------------------------------------
[testng] [2024-10-08 10:06:30,147] [main] Total files: 15
[testng] [2024-10-08 10:06:30,147] [main] Scan time: 0.989 s (65 ms/file)
[testng] [2024-10-08 10:06:30,147] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 15 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-10-08 10:06:45,680] [pool-1-thread-1] Initializing /data/samples/ICBM/icbm_template_6.00mm.mnc:
[testng] 10:06:45,681 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 10:06:45,681 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:06:45,683 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-08_10-06-45.log]
[testng] 10:06:45,683 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43efff27 - End of configuration.
[testng] [2024-10-08 10:06:46,267] [pool-1-thread-12] Initializing /data/samples/ICBM/icbm_template_zero.50mm.mnc:
[testng] 10:06:46,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 10:06:46,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:06:46,268 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-08_10-06-46.log]
[testng] 10:06:46,268 |-INFO in ch.qos.logback.core.sift.SiftProcessor@462c7c3a - End of configuration.
[testng] [2024-10-08 10:06:46,925] [pool-1-thread-11] Initializing /data/samples/ICBM/icbm_atlas_cerebellum_avg_53_mask_1mm.mnc:
[testng] 10:06:46,925 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 10:06:46,925 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:06:46,926 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-08_10-06-46.log]
[testng] 10:06:46,926 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27cea7f3 - End of configuration.
[testng] [2024-10-08 10:06:47,501] [pool-1-thread-10] Initializing /data/samples/ICBM/icbm_template_4.00mm.mnc:
[testng] 10:06:47,501 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 10:06:47,501 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:06:47,502 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-08_10-06-47.log]
[testng] 10:06:47,502 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c358dd4 - End of configuration.
[testng] [2024-10-08 10:06:48,086] [pool-1-thread-9] Initializing /data/samples/ICBM/icbm_template_one.00mm.mnc:
[testng] 10:06:48,086 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 10:06:48,086 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:06:48,087 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-08_10-06-48.log]
[testng] 10:06:48,087 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73c9adfc - End of configuration.
[testng] [2024-10-08 10:06:48,758] [pool-1-thread-8] Initializing /data/samples/ICBM/icbm_template_one.50mm.mnc:
[testng] 10:06:48,758 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 10:06:48,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:06:48,759 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-08_10-06-48.log]
[testng] 10:06:48,760 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68bad2d9 - End of configuration.
[testng] [2024-10-08 10:06:49,401] [pool-1-thread-7] Initializing /data/samples/ICBM/icbm_template_2.00mm.mnc:
[testng] 10:06:49,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 10:06:49,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:06:49,402 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-08_10-06-49.log]
[testng] 10:06:49,402 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53f5c625 - End of configuration.
[testng] [2024-10-08 10:06:50,112] [pool-1-thread-6] Initializing /data/samples/ICBM/icbm_template_zero.75mm.mnc:
[testng] 10:06:50,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 10:06:50,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:06:50,113 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-08_10-06-50.log]
[testng] 10:06:50,113 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2939ecc9 - End of configuration.
[testng] [2024-10-08 10:06:50,853] [pool-1-thread-5] Initializing /data/bigbrain/pm6479o.mnc:
[testng] 10:06:50,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 10:06:50,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:06:50,854 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-08_10-06-50.log]
[testng] 10:06:50,855 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28cdffc7 - End of configuration.
[testng] [2024-10-08 10:06:51,997] [pool-1-thread-4] Initializing /data/samples/ICBM/icbm_template_3.00mm.mnc:
[testng] 10:06:51,997 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 10:06:51,997 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:06:51,998 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-08_10-06-51.log]
[testng] 10:06:51,998 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48e00598 - End of configuration.
[testng] [2024-10-08 10:06:52,819] [pool-1-thread-3] Initializing /data/qa-17215/IBSR01.mnc:
[testng] 10:06:52,819 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 10:06:52,819 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:06:52,820 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-08_10-06-52.log]
[testng] 10:06:52,821 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61f58cd7 - End of configuration.
[testng] [2024-10-08 10:06:53,706] [pool-1-thread-2] Initializing /data/samples/N3/average_305_mask_1mm.mnc:
[testng] 10:06:53,706 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 10:06:53,706 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:06:53,707 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-08_10-06-53.log]
[testng] 10:06:53,707 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73570c23 - End of configuration.
BUILD SUCCESSFUL
Total time: 1 minute 1 second
Finished: SUCCESS