Started by upstream project "BIOFORMATS-test-repo" build number 282
originally caused by:
Started by user devspace
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder
[BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins3414739033456080065.sh
+ '[' leica = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_44436_merge_ci -v /uod/idr/repos/curated/leica:/data -v /uod/idr-scratch/merge-ci/curated/leica:/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] 10:10:55,785 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 10:10:55,787 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service.
[testng] 10:10:55,787 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 10:10:55,788 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 10:10:55,788 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 10:10:55,788 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 10:10:55,788 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 10:10:55,788 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 10:10:55,789 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 10:10:55,789 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 10:10:55,789 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 10:10:55,789 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 10:10:56,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 10:10:56,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 10:10:56,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 10:10:56,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 10:10:56,148 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 10:10:56,148 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 10:10:56,149 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 10:10:56,149 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 10:10:56,149 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration.
[testng] 10:10:56,150 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point
[testng] 10:10:56,150 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 361 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-12-06 10:10:56,160] [main] java.version = 1.8.0_342
[testng] 10:10:56,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 10:10:56,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:10:56,253 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-06_10-10-56.log]
[testng] 10:10:56,255 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration.
[testng] [2024-12-06 10:10:56,256] [main] testng.directory = /data
[testng] [2024-12-06 10:10:56,257] [main] testng.configDirectory = /config
[testng] [2024-12-06 10:10:56,292] [main] testng.multiplier = 1.0
[testng] [2024-12-06 10:10:56,292] [main] testng.in-memory = false
[testng] [2024-12-06 10:10:56,292] [main] testng.allow-missing = false
[testng] [2024-12-06 10:10:56,292] [main] user.language = en
[testng] [2024-12-06 10:10:56,292] [main] user.country = ${user.country}
[testng] [2024-12-06 10:10:56,292] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-12-06 10:11:12,881] [main] ----------------------------------------
[testng] [2024-12-06 10:11:12,882] [main] Total files: 5651
[testng] [2024-12-06 10:11:12,882] [main] Scan time: 16.589 s (2 ms/file)
[testng] [2024-12-06 10:11:12,882] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 44 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-12-06 10:12:01,960] [pool-1-thread-1] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei:
[testng] 10:12:01,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 10:12:01,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:12:01,962 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-06_10-12-01.log]
[testng] 10:12:01,962 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f48ff9 - End of configuration.
[testng] [2024-12-06 10:12:02,452] [pool-1-thread-12] Initializing /data/samples/Leica_sample.lei:
[testng] 10:12:02,453 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 10:12:02,453 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:12:02,453 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-06_10-12-02.log]
[testng] 10:12:02,454 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79dd0a38 - End of configuration.
[testng] [2024-12-06 10:12:02,940] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg:
[testng] 10:12:02,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 10:12:02,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:12:02,941 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-06_10-12-02.log]
[testng] 10:12:02,941 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d78f1f6 - End of configuration.
[testng] [2024-12-06 10:12:02,981] [pool-1-thread-10] Initializing /data/simon/Leica demo/test/test.lei:
[testng] 10:12:02,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 10:12:02,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:12:02,982 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-06_10-12-02.log]
[testng] 10:12:02,982 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14d4338c - End of configuration.
[testng] [2024-12-06 10:12:03,309] [pool-1-thread-9] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei:
[testng] 10:12:03,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 10:12:03,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:12:03,309 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-06_10-12-03.log]
[testng] 10:12:03,310 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e0500e2 - End of configuration.
[testng] [2024-12-06 10:12:03,789] [pool-1-thread-8] Initializing /data/joel/sequential scan 3/sequential scan 3.lei:
[testng] 10:12:03,789 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 10:12:03,790 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:12:03,790 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-06_10-12-03.log]
[testng] 10:12:03,791 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ec6ad00 - End of configuration.
[testng] [2024-12-06 10:12:04,092] [pool-1-thread-7] Initializing /data/constantin/cell6/Quant_Image_01.jpg:
[testng] 10:12:04,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 10:12:04,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:12:04,093 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-06_10-12-04.log]
[testng] 10:12:04,093 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a1bc1c9 - End of configuration.
[testng] [2024-12-06 10:12:04,139] [pool-1-thread-6] Initializing /data/constantin/cell6/Quant_Image_02.jpg:
[testng] 10:12:04,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 10:12:04,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:12:04,140 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-06_10-12-04.log]
[testng] 10:12:04,141 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e6b8f85 - End of configuration.
[testng] [2024-12-06 10:12:04,190] [pool-1-thread-5] Initializing /data/christophe/Leica stacks/Nf5.lei:
[testng] 10:12:04,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 10:12:04,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:12:04,191 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-06_10-12-04.log]
[testng] 10:12:04,191 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f7faf5c - End of configuration.
[testng] [2024-12-06 10:12:04,579] [pool-1-thread-4] Initializing /data/joel/sequential scan 2/sequential scan 2.lei:
[testng] 10:12:04,579 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 10:12:04,579 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:12:04,579 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-06_10-12-04.log]
[testng] 10:12:04,580 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d5a0caa - End of configuration.
[testng] [2024-12-06 10:12:04,945] [pool-1-thread-3] Initializing /data/brian/050627-leica/050628-leica.lei:
[testng] 10:12:04,945 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 10:12:04,945 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:12:04,945 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-06_10-12-04.log]
[testng] 10:12:04,946 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ecdc4a6 - End of configuration.
[testng] [2024-12-06 10:12:06,107] [pool-1-thread-2] Initializing /data/julie/biorad/8291mcd8_raw01.pic:
[testng] 10:12:06,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 10:12:06,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:12:06,108 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-06_10-12-06.log]
[testng] 10:12:06,108 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c94e66 - End of configuration.
[testng] [2024-12-06 10:12:09,460] [pool-1-thread-7] Initializing /data/david/megan/megan.lei:
[testng] [2024-12-06 10:12:10,546] [pool-1-thread-6] Initializing /data/stjude/NIHSSE02-3.lei:
[testng] [2024-12-06 10:12:11,481] [pool-1-thread-11] Initializing /data/julie/c164_1.tif:
[testng] [2024-12-06 10:12:18,721] [pool-1-thread-2] Initializing /data/mark/071026-561nm check/071026-561nm check.lei:
[testng] [2024-12-06 10:12:19,769] [pool-1-thread-12] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif:
[testng] [2024-12-06 10:12:22,161] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6.lei:
[testng] [2024-12-06 10:12:23,059] [pool-1-thread-1] Initializing /data/constantin/cell6/Logo.jpg:
[testng] [2024-12-06 10:12:26,481] [pool-1-thread-1] Initializing /data/andrey/10310500/10310500.lei:
[testng] [2024-12-06 10:12:30,401] [pool-1-thread-12] Initializing /data/clay/leica_stack.tif:
[testng] [2024-12-06 10:12:36,741] [pool-1-thread-12] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei:
[testng] [2024-12-06 10:13:17,430] [pool-1-thread-6] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg:
[testng] [2024-12-06 10:13:19,342] [pool-1-thread-6] Initializing /data/constantin/cell6/Graphs_1_00.jpg:
[testng] [2024-12-06 10:13:21,730] [pool-1-thread-6] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei:
[testng] [2024-12-06 10:14:48,872] [pool-1-thread-5] Initializing /data/brian/leica-original/050118.lei:
[testng] [2024-12-06 10:15:11,863] [pool-1-thread-9] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif:
[testng] [2024-12-06 10:15:16,046] [pool-1-thread-12] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei:
[testng] [2024-12-06 10:15:20,169] [pool-1-thread-9] Initializing /data/simon/Leica demo/fish/fish.lei:
[testng] [2024-12-06 10:17:48,353] [pool-1-thread-4] Initializing /data/oliver/o459/o459.lei:
[testng] [2024-12-06 10:17:54,271] [pool-1-thread-8] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei:
[testng] [2024-12-06 10:18:04,673] [pool-1-thread-11] Initializing /data/martin/samples-SP2/samples-SP2.lei:
[testng] [2024-12-06 10:18:36,597] [pool-1-thread-7] Initializing /data/brian/tropo/tropo.lei:
[testng] [2024-12-06 10:18:56,703] [pool-1-thread-7] Initializing /data/clay/leica_stack.lei:
[testng] [2024-12-06 10:19:06,633] [pool-1-thread-2] Initializing /data/constantin/cell6/cell6/Logo.jpg:
[testng] [2024-12-06 10:19:08,441] [pool-1-thread-7] Initializing /data/david/intestine/intestine.lei:
[testng] [2024-12-06 10:19:10,112] [pool-1-thread-2] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei:
[testng] [2024-12-06 10:19:30,166] [pool-1-thread-10] Initializing /data/michael/2007-01-31_zres_sp2.lei:
[testng] [2024-12-06 10:19:46,789] [pool-1-thread-10] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei:
[testng] [2024-12-06 10:20:42,879] [pool-1-thread-8] Initializing /data/grant/Leica SP2 (25-11-10).lei:
[testng] [2024-12-06 10:21:36,856] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg:
[testng] [2024-12-06 10:21:38,649] [pool-1-thread-1] Initializing /data/vytas/4voxels/4voxels.lei:
[testng] [2024-12-06 10:22:27,507] [pool-1-thread-3] Initializing /data/constantin/cell6/Quant_Image_00.jpg:
[testng] [2024-12-06 10:22:27,698] [pool-1-thread-12] Initializing /data/julie/biorad/25-65.tif:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 2332, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 60 minutes 8 seconds
Finished: SUCCESS