Started by upstream project "BIOFORMATS-test-repo" build number 273
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/jenkins13523520192951224354.sh
+ '[' imaris = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_43076_merge_ci -v /uod/idr/repos/curated/imaris:/data -v /uod/idr-scratch/merge-ci/curated/imaris:/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
test-automated:
[testng] File leak detector installed
[testng] 10:13:15,477 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 10:13:15,478 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service.
[testng] 10:13:15,478 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 10:13:15,479 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 10:13:15,479 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 10:13:15,479 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 10:13:15,480 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 10:13:15,480 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 10:13:15,480 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 10:13:15,480 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 10:13:15,481 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 10:13:15,481 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 10:13:15,690 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 10:13:15,690 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 10:13:15,715 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 10:13:15,715 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 10:13:15,722 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 10:13:15,722 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 10:13:15,723 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 10:13:15,723 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 10:13:15,723 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration.
[testng] 10:13:15,724 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point
[testng] 10:13:15,724 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 244 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-11-29 10:13:15,733] [main] java.version = 1.8.0_342
[testng] 10:13:15,737 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 10:13:15,737 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:13:15,779 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-29_10-13-15.log]
[testng] 10:13:15,780 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration.
[testng] [2024-11-29 10:13:15,782] [main] testng.directory = /data
[testng] [2024-11-29 10:13:15,782] [main] testng.configDirectory = /config
[testng] [2024-11-29 10:13:15,793] [main] testng.multiplier = 1.0
[testng] [2024-11-29 10:13:15,793] [main] testng.in-memory = false
[testng] [2024-11-29 10:13:15,793] [main] testng.allow-missing = false
[testng] [2024-11-29 10:13:15,793] [main] user.language = en
[testng] [2024-11-29 10:13:15,793] [main] user.country = ${user.country}
[testng] [2024-11-29 10:13:15,793] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-11-29 10:14:20,607] [main] ----------------------------------------
[testng] [2024-11-29 10:14:20,607] [main] Total files: 71
[testng] [2024-11-29 10:14:20,607] [main] Scan time: 64.814 s (912 ms/file)
[testng] [2024-11-29 10:14:20,607] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 62 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-11-29 10:15:59,288] [pool-1-thread-1] Initializing /data/jason/imaris_5_5_demoimages/HeLaCell.ims:
[testng] 10:15:59,289 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 10:15:59,289 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:15:59,290 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-29_10-15-59.log]
[testng] 10:15:59,290 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f55e608 - End of configuration.
[testng] [2024-11-29 10:16:00,043] [pool-1-thread-12] Initializing /data/generated/10-31_E_t0004.ims:
[testng] 10:16:00,043 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 10:16:00,043 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:16:00,044 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-29_10-16-00.log]
[testng] 10:16:00,044 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57fdeba2 - End of configuration.
[testng] [2024-11-29 10:16:00,445] [pool-1-thread-11] Initializing /data/public/davemason/Convallaria_3C_3T_2x2grid_confocal_IMS3.ims:
[testng] 10:16:00,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 10:16:00,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:16:00,446 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-29_10-16-00.log]
[testng] 10:16:00,446 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fabb009 - End of configuration.
[testng] [2024-11-29 10:16:01,533] [pool-1-thread-10] Initializing /data/generated/10-31_E_t0013.ims:
[testng] 10:16:01,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 10:16:01,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:16:01,534 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-29_10-16-01.log]
[testng] 10:16:01,534 |-INFO in ch.qos.logback.core.sift.SiftProcessor@cc93dc6 - End of configuration.
[testng] [2024-11-29 10:16:01,965] [pool-1-thread-9] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal_deconvolved_IMS3.ims:
[testng] 10:16:01,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 10:16:01,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:16:01,966 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-29_10-16-01.log]
[testng] 10:16:01,966 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a748394 - End of configuration.
[testng] [2024-11-29 10:16:03,222] [pool-1-thread-8] Initializing /data/jcb/fig 6B GFP-AP-2d.ims:
[testng] 10:16:03,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 10:16:03,222 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:16:03,223 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-29_10-16-03.log]
[testng] 10:16:03,223 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bce53ef - End of configuration.
[testng] [2024-11-29 10:16:04,920] [pool-1-thread-7] Initializing /data/generated/10-31_E_t0010.ims:
[testng] 10:16:04,920 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 10:16:04,920 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:16:04,921 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-29_10-16-04.log]
[testng] 10:16:04,921 |-INFO in ch.qos.logback.core.sift.SiftProcessor@523208f9 - End of configuration.
[testng] [2024-11-29 10:16:05,337] [pool-1-thread-6] Initializing /data/public/eliana/retina_large.ims:
[testng] 10:16:05,337 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 10:16:05,337 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:16:05,338 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-29_10-16-05.log]
[testng] 10:16:05,356 |-INFO in ch.qos.logback.core.sift.SiftProcessor@91f5fad - End of configuration.
[testng] [2024-11-29 10:16:06,965] [pool-1-thread-5] Initializing /data/public/eliana/2016-07-26_17.11.03_Sample Prefix_5P298C2_Protocol.ims:
[testng] 10:16:06,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 10:16:06,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:16:06,966 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-29_10-16-06.log]
[testng] 10:16:06,966 |-INFO in ch.qos.logback.core.sift.SiftProcessor@413a1f2e - End of configuration.
[testng] [2024-11-29 10:16:08,168] [pool-1-thread-4] Initializing /data/public/davemason/Convallaria_3C_10T_confocal_IMS3.ims:
[testng] 10:16:08,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 10:16:08,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:16:08,169 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-29_10-16-08.log]
[testng] 10:16:08,169 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f9a69bc - End of configuration.
[testng] [2024-11-29 10:16:09,098] [pool-1-thread-3] Initializing /data/oliver/Stack2_u16Bit.ims:
[testng] 10:16:09,098 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 10:16:09,098 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:16:09,099 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-29_10-16-09.log]
[testng] 10:16:09,099 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c659164 - End of configuration.
[testng] [2024-11-29 10:16:09,924] [pool-1-thread-2] Initializing /data/generated/MF-2CH-Z-T.ims:
[testng] 10:16:09,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 10:16:09,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:16:09,925 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-29_10-16-09.log]
[testng] 10:16:09,925 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e5dd62c - End of configuration.
[testng] [2024-11-29 10:16:16,101] [pool-1-thread-12] Initializing /data/public/davemason/Convallaria_3C_1T_2x2grid_confocal_IMS3.ims:
[testng] [2024-11-29 10:16:16,887] [pool-1-thread-10] Initializing /data/generated/10-31_E_t0008.ims:
[testng] [2024-11-29 10:16:17,175] [pool-1-thread-7] Initializing /data/generated/10-31_E_t0000.ims:
[testng] [2024-11-29 10:16:18,615] [pool-1-thread-1] Initializing /data/public/davemason/TransFactors_2C_34Z_SRRF.ims:
BUILD SUCCESSFUL
Total time: 5 minutes 13 seconds
Finished: SUCCESS