Started by upstream project "BIOFORMATS-test-repo" build number 97
originally caused by:
Started by upstream project "Trigger" build number 108
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/jenkins8264728400819359019.sh
+ '[' minc = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_14969_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] 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] 01:44:18,626 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:44:18,628 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service.
[testng] 01:44:18,628 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:44:18,629 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:44:18,629 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:44:18,630 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:44:18,630 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:44:18,630 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:44:18,631 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:44:18,631 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:44:18,632 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:44:18,632 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:44:18,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:44:18,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:44:18,837 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:44:18,837 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:44:18,843 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:44:18,843 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:44:18,843 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:44:18,843 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:44:18,843 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration.
[testng] 01:44:18,844 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point
[testng] 01:44:18,844 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 213 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-06-19 01:44:18,853] [main] java.version = 17.0.2
[testng] 01:44:18,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:44:18,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:18,917 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-19_01-44-18.log]
[testng] 01:44:18,920 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration.
[testng] [2024-06-19 01:44:18,923] [main] testng.directory = /data
[testng] [2024-06-19 01:44:18,924] [main] testng.configDirectory = /config
[testng] [2024-06-19 01:44:18,940] [main] testng.multiplier = 1.0
[testng] [2024-06-19 01:44:18,941] [main] testng.in-memory = false
[testng] [2024-06-19 01:44:18,941] [main] testng.allow-missing = false
[testng] [2024-06-19 01:44:18,941] [main] user.language = en
[testng] [2024-06-19 01:44:18,941] [main] user.country = ${user.country}
[testng] [2024-06-19 01:44:18,941] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-06-19 01:44:19,353] [main] ----------------------------------------
[testng] [2024-06-19 01:44:19,353] [main] Total files: 15
[testng] [2024-06-19 01:44:19,353] [main] Scan time: 0.412 s (27 ms/file)
[testng] [2024-06-19 01:44:19,353] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 15 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-06-19 01:44:26,161] [pool-1-thread-1] Initializing /data/samples/ICBM/icbm_template_3.00mm.mnc:
[testng] 01:44:26,162 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:44:26,162 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:26,163 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-19_01-44-26.log]
[testng] 01:44:26,163 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6aa1c309 - End of configuration.
[testng] [2024-06-19 01:44:26,187] [pool-1-thread-12] Initializing /data/bigbrain/8-bit_full_400um_2009b_sym.mnc:
[testng] 01:44:26,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:44:26,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:26,188 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-19_01-44-26.log]
[testng] 01:44:26,189 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46af4b0e - End of configuration.
[testng] [2024-06-19 01:44:27,199] [pool-1-thread-11] Initializing /data/bigbrain/pm6479o.mnc:
[testng] 01:44:27,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:44:27,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:27,201 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-19_01-44-27.log]
[testng] 01:44:27,201 |-INFO in ch.qos.logback.core.sift.SiftProcessor@345592b9 - End of configuration.
[testng] [2024-06-19 01:44:27,788] [pool-1-thread-10] Initializing /data/samples/ICBM/icbm_template_2.00mm.mnc:
[testng] 01:44:27,789 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:44:27,789 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:27,790 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-19_01-44-27.log]
[testng] 01:44:27,790 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47b271ac - End of configuration.
[testng] [2024-06-19 01:44:27,803] [pool-1-thread-9] Initializing /data/qa-17215/IBSR01.mnc:
[testng] 01:44:27,803 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:44:27,803 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:27,804 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-19_01-44-27.log]
[testng] 01:44:27,805 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b44a3e9 - End of configuration.
[testng] [2024-06-19 01:44:27,895] [pool-1-thread-8] Initializing /data/samples/ICBM/icbm_template_4.00mm.mnc:
[testng] 01:44:27,895 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:44:27,896 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:27,896 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-19_01-44-27.log]
[testng] 01:44:27,897 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ad170ca - End of configuration.
[testng] [2024-06-19 01:44:27,906] [pool-1-thread-7] Initializing /data/daren/test_32bit_float.mnc:
[testng] 01:44:27,906 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:44:27,906 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:27,906 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-19_01-44-27.log]
[testng] 01:44:27,907 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5876cc97 - End of configuration.
[testng] [2024-06-19 01:44:28,235] [pool-1-thread-6] Initializing /data/samples/ICBM/icbm_atlas_cerebellum_avg_53_mask_1mm.mnc:
[testng] 01:44:28,235 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:44:28,235 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:28,236 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-19_01-44-28.log]
[testng] 01:44:28,236 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a5e72b1 - End of configuration.
[testng] [2024-06-19 01:44:28,272] [pool-1-thread-5] Initializing /data/samples/ICBM/icbm_template_zero.75mm.mnc:
[testng] 01:44:28,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:44:28,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:28,273 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-19_01-44-28.log]
[testng] 01:44:28,274 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64d791c4 - End of configuration.
[testng] [2024-06-19 01:44:28,317] [pool-1-thread-4] Initializing /data/samples/N3/average_305_mask_1mm.mnc:
[testng] 01:44:28,317 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:44:28,317 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:28,318 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-19_01-44-28.log]
[testng] 01:44:28,319 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48365b90 - End of configuration.
[testng] [2024-06-19 01:44:28,354] [pool-1-thread-3] Initializing /data/samples/ICBM/icbm_template_one.50mm.mnc:
[testng] 01:44:28,355 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:44:28,355 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:28,355 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-19_01-44-28.log]
[testng] 01:44:28,356 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f56a4c6 - End of configuration.
[testng] [2024-06-19 01:44:28,368] [pool-1-thread-2] Initializing /data/samples/ICBM/icbm_template_6.00mm.mnc:
[testng] 01:44:28,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:44:28,369 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:44:28,369 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-19_01-44-28.log]
[testng] 01:44:28,370 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36f7c500 - End of configuration.
BUILD SUCCESSFUL
Total time: 33 seconds
Finished: SUCCESS