Started by upstream project "BIOFORMATS-test-repo" build number 294
originally caused by:
Started by upstream project "Trigger" build number 313
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@10
[BIOFORMATS-test-folder@10] $ /bin/bash -xe /tmp/jenkins10058984241297287430.sh
+ '[' nrrd = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_46518_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] 10:45:05,245 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 10:45:05,246 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service.
[testng] 10:45:05,246 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 10:45:05,247 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 10:45:05,248 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 10:45:05,248 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 10:45:05,248 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 10:45:05,248 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 10:45:05,249 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 10:45:05,249 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 10:45:05,249 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 10:45:05,250 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 10:45:05,397 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 10:45:05,397 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 10:45:05,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 10:45:05,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 10:45:05,422 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 10:45:05,422 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 10:45:05,422 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 10:45:05,422 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 10:45:05,422 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration.
[testng] 10:45:05,423 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point
[testng] 10:45:05,423 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 174 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-12-18 10:45:05,431] [main] java.version = 17.0.2
[testng] 10:45:05,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 10:45:05,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:45:05,470 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-18_10-45-05.log]
[testng] 10:45:05,471 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration.
[testng] [2024-12-18 10:45:05,473] [main] testng.directory = /data
[testng] [2024-12-18 10:45:05,473] [main] testng.configDirectory = /config
[testng] [2024-12-18 10:45:05,481] [main] testng.multiplier = 1.0
[testng] [2024-12-18 10:45:05,482] [main] testng.in-memory = false
[testng] [2024-12-18 10:45:05,482] [main] testng.allow-missing = false
[testng] [2024-12-18 10:45:05,482] [main] user.language = en
[testng] [2024-12-18 10:45:05,482] [main] user.country = ${user.country}
[testng] [2024-12-18 10:45:05,483] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-12-18 10:47:01,243] [main] ----------------------------------------
[testng] [2024-12-18 10:47:01,243] [main] Total files: 14
[testng] [2024-12-18 10:47:01,243] [main] Scan time: 115.76 s (8268 ms/file)
[testng] [2024-12-18 10:47:01,243] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 10 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-12-18 10:47:22,578] [pool-1-thread-1] Initializing /data/greg/average-goodbrains-warp40-5_e1e-2.PIC.nhdr:
[testng] 10:47:22,578 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 10:47:22,578 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:47:22,579 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-18_10-47-22.log]
[testng] 10:47:22,579 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39a5f86f - End of configuration.
[testng] [2024-12-18 10:47:23,546] [pool-1-thread-10] Initializing /data/public/gordon/gk2-rcc-mask.nhdr:
[testng] 10:47:23,546 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 10:47:23,546 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:47:23,548 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-18_10-47-23.log]
[testng] 10:47:23,548 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15476813 - End of configuration.
[testng] [2024-12-18 10:47:24,527] [pool-1-thread-9] Initializing /data/public/glencoe/version4/dt-helix.nhdr:
[testng] 10:47:24,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 10:47:24,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:47:24,529 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-18_10-47-24.log]
[testng] 10:47:24,529 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67b43042 - End of configuration.
[testng] [2024-12-18 10:47:25,430] [pool-1-thread-8] Initializing /data/public/gordon/gk2-rcc-mask2.nhdr:
[testng] 10:47:25,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 10:47:25,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:47:25,431 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-18_10-47-25.log]
[testng] 10:47:25,432 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f131a36 - End of configuration.
[testng] [2024-12-18 10:47:26,298] [pool-1-thread-7] Initializing /data/greg/average-goodbrains-warp40-5_e1e-2.PIC.gz.nhdr:
[testng] 10:47:26,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 10:47:26,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:47:26,299 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-18_10-47-26.log]
[testng] 10:47:26,300 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7057ca89 - End of configuration.
[testng] [2024-12-18 10:47:27,118] [pool-1-thread-6] Initializing /data/greg/average-goodbrains-warp40-5_e1e-2.am.nrrd:
[testng] 10:47:27,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 10:47:27,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:47:27,118 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-18_10-47-27.log]
[testng] 10:47:27,119 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1032b5ee - End of configuration.
[testng] [2024-12-18 10:47:28,142] [pool-1-thread-5] Initializing /data/carlos/big4DImage.nrrd:
[testng] 10:47:28,142 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 10:47:28,142 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:47:28,142 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-18_10-47-28.log]
[testng] 10:47:28,143 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58f75cd7 - End of configuration.
[testng] [2024-12-18 10:47:29,127] [pool-1-thread-4] Initializing /data/public/glencoe/gzip/dt-helix.nrrd.gz:
[testng] 10:47:29,127 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 10:47:29,127 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:47:29,128 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-18_10-47-29.log]
[testng] 10:47:29,128 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34492fa9 - End of configuration.
[testng] [2024-12-18 10:47:31,073] [pool-1-thread-3] Initializing /data/public/gordon/dt-helix.nhdr:
[testng] 10:47:31,074 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 10:47:31,074 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:47:31,074 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-18_10-47-31.log]
[testng] 10:47:31,075 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2907bac3 - End of configuration.
[testng] [2024-12-18 10:47:31,952] [pool-1-thread-2] Initializing /data/public/midas/01011-dwi.nhdr:
[testng] 10:47:31,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 10:47:31,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:47:31,953 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-18_10-47-31.log]
[testng] 10:47:31,954 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c3d5a57 - 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: 4 minutes 17 seconds
Finished: SUCCESS