Started by upstream project "BIOFORMATS-test-repo" build number 207
originally caused by:
Started by upstream project "Trigger" build number 233
originally caused by:
Started by timer
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/jenkins6984918062355681957.sh
+ '[' minc = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_32852_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] 04:12:20,602 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 04:12:20,603 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service.
[testng] 04:12:20,603 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 04:12:20,604 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 04:12:20,604 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 04:12:20,605 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 04:12:20,605 |-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] 04:12:20,605 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 04:12:20,605 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 04:12:20,606 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 04:12:20,606 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 04:12:20,606 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 04:12:20,766 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 04:12:20,766 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 04:12:20,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 04:12:20,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 04:12:20,794 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 04:12:20,794 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 04:12:20,794 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 04:12:20,794 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 04:12:20,794 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration.
[testng] 04:12:20,795 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point
[testng] 04:12:20,796 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 191 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-10-02 04:12:20,804] [main] java.version = 17.0.2
[testng] 04:12:20,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 04:12:20,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:12:20,847 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-02_04-12-20.log]
[testng] 04:12:20,849 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration.
[testng] [2024-10-02 04:12:20,851] [main] testng.directory = /data
[testng] [2024-10-02 04:12:20,851] [main] testng.configDirectory = /config
[testng] [2024-10-02 04:12:20,859] [main] testng.multiplier = 1.0
[testng] [2024-10-02 04:12:20,860] [main] testng.in-memory = false
[testng] [2024-10-02 04:12:20,860] [main] testng.allow-missing = false
[testng] [2024-10-02 04:12:20,861] [main] user.language = en
[testng] [2024-10-02 04:12:20,861] [main] user.country = ${user.country}
[testng] [2024-10-02 04:12:20,861] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-10-02 04:12:24,306] [main] ----------------------------------------
[testng] [2024-10-02 04:12:24,306] [main] Total files: 15
[testng] [2024-10-02 04:12:24,306] [main] Scan time: 3.445 s (229 ms/file)
[testng] [2024-10-02 04:12:24,306] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 15 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-10-02 04:12:44,588] [pool-1-thread-1] Initializing /data/samples/ICBM/icbm_template_2.00mm.mnc:
[testng] 04:12:44,589 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 04:12:44,589 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:12:44,591 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-02_04-12-44.log]
[testng] 04:12:44,591 |-INFO in ch.qos.logback.core.sift.SiftProcessor@174e2671 - End of configuration.
[testng] [2024-10-02 04:12:45,707] [pool-1-thread-12] Initializing /data/daren/test_32bit_float.mnc:
[testng] 04:12:45,707 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 04:12:45,707 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:12:45,708 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-02_04-12-45.log]
[testng] 04:12:45,709 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78be4bcc - End of configuration.
[testng] [2024-10-02 04:12:47,153] [pool-1-thread-11] Initializing /data/samples/ICBM/icbm_template_one.50mm.mnc:
[testng] 04:12:47,153 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 04:12:47,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:12:47,155 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-02_04-12-47.log]
[testng] 04:12:47,155 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48e5605f - End of configuration.
[testng] [2024-10-02 04:12:48,116] [pool-1-thread-10] Initializing /data/samples/ICBM/icbm_template_zero.50mm.mnc:
[testng] 04:12:48,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 04:12:48,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:12:48,117 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-02_04-12-48.log]
[testng] 04:12:48,118 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5433b13f - End of configuration.
[testng] [2024-10-02 04:12:49,244] [pool-1-thread-9] Initializing /data/samples/ICBM/icbm_template_6.00mm.mnc:
[testng] 04:12:49,244 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 04:12:49,244 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:12:49,245 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-02_04-12-49.log]
[testng] 04:12:49,245 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4aae8575 - End of configuration.
[testng] [2024-10-02 04:12:50,401] [pool-1-thread-8] Initializing /data/samples/ICBM/icbm_template_3.00mm.mnc:
[testng] 04:12:50,402 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 04:12:50,402 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:12:50,402 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-02_04-12-50.log]
[testng] 04:12:50,403 |-INFO in ch.qos.logback.core.sift.SiftProcessor@178552de - End of configuration.
[testng] [2024-10-02 04:12:51,287] [pool-1-thread-7] Initializing /data/samples/ICBM/icbm_template_zero.75mm.mnc:
[testng] 04:12:51,287 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 04:12:51,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:12:51,288 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-02_04-12-51.log]
[testng] 04:12:51,289 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ae2b6c7 - End of configuration.
[testng] [2024-10-02 04:12:52,062] [pool-1-thread-6] Initializing /data/qa-17215/IBSR01.mnc:
[testng] 04:12:52,062 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 04:12:52,062 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:12:52,063 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-02_04-12-52.log]
[testng] 04:12:52,063 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4332bba0 - End of configuration.
[testng] [2024-10-02 04:12:53,110] [pool-1-thread-5] Initializing /data/samples/ICBM/icbm_atlas_cerebellum_avg_53_mask_1mm.mnc:
[testng] 04:12:53,111 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 04:12:53,111 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:12:53,111 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-02_04-12-53.log]
[testng] 04:12:53,112 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7669c3b7 - End of configuration.
[testng] [2024-10-02 04:12:54,725] [pool-1-thread-4] Initializing /data/samples/ICBM/icbm_template_4.00mm.mnc:
[testng] 04:12:54,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 04:12:54,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:12:54,725 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-02_04-12-54.log]
[testng] 04:12:54,726 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a9ce216 - End of configuration.
[testng] [2024-10-02 04:12:55,665] [pool-1-thread-3] Initializing /data/bigbrain/pm6479o.mnc:
[testng] 04:12:55,666 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 04:12:55,666 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:12:55,666 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-02_04-12-55.log]
[testng] 04:12:55,667 |-INFO in ch.qos.logback.core.sift.SiftProcessor@313594dc - End of configuration.
[testng] [2024-10-02 04:12:57,223] [pool-1-thread-2] Initializing /data/bigbrain/8-bit_full_400um_2009b_sym.mnc:
[testng] 04:12:57,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 04:12:57,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:12:57,224 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-02_04-12-57.log]
[testng] 04:12:57,224 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35b4d601 - End of configuration.
BUILD SUCCESSFUL
Total time: 1 minute 31 seconds
Finished: SUCCESS