Started by upstream project "BIOFORMATS-test-repo" build number 85
originally caused by:
Started by upstream project "Trigger" build number 96
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/jenkins262871374004642401.sh
+ '[' leica = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_12928_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] 01:21:02,785 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:21:02,786 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service.
[testng] 01:21:02,786 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:21:02,787 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:21:02,787 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:21:02,787 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:21:02,788 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:21:02,788 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:21:02,788 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:21:02,788 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:21:02,788 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:21:02,788 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:21:03,062 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:21:03,062 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:21:03,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:21:03,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:21:03,113 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:21:03,114 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:21:03,114 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:21:03,114 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:21:03,114 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration.
[testng] 01:21:03,115 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point
[testng] 01:21:03,115 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 327 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-06-07 01:21:03,124] [main] java.version = 1.8.0_342
[testng] 01:21:03,127 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:21:03,127 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:03,169 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-07_01-21-03.log]
[testng] 01:21:03,170 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration.
[testng] [2024-06-07 01:21:03,172] [main] testng.directory = /data
[testng] [2024-06-07 01:21:03,172] [main] testng.configDirectory = /config
[testng] [2024-06-07 01:21:03,184] [main] testng.multiplier = 1.0
[testng] [2024-06-07 01:21:03,184] [main] testng.in-memory = false
[testng] [2024-06-07 01:21:03,184] [main] testng.allow-missing = false
[testng] [2024-06-07 01:21:03,184] [main] user.language = en
[testng] [2024-06-07 01:21:03,184] [main] user.country = ${user.country}
[testng] [2024-06-07 01:21:03,184] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-06-07 01:21:10,356] [main] ----------------------------------------
[testng] [2024-06-07 01:21:10,357] [main] Total files: 5651
[testng] [2024-06-07 01:21:10,357] [main] Scan time: 7.172 s (1 ms/file)
[testng] [2024-06-07 01:21:10,357] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 44 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-06-07 01:21:26,228] [pool-1-thread-1] Initializing /data/mark/071026-561nm check/071026-561nm check.lei:
[testng] 01:21:26,229 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:21:26,229 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:26,230 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-07_01-21-26.log]
[testng] 01:21:26,231 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ec6a625 - End of configuration.
[testng] [2024-06-07 01:21:26,339] [pool-1-thread-12] Initializing /data/constantin/cell6/Quant_Image_02.jpg:
[testng] 01:21:26,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:21:26,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:26,340 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-07_01-21-26.log]
[testng] 01:21:26,340 |-INFO in ch.qos.logback.core.sift.SiftProcessor@644e3908 - End of configuration.
[testng] [2024-06-07 01:21:26,348] [pool-1-thread-11] Initializing /data/simon/Leica demo/test/test.lei:
[testng] 01:21:26,348 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:21:26,348 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:26,349 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-07_01-21-26.log]
[testng] 01:21:26,349 |-INFO in ch.qos.logback.core.sift.SiftProcessor@705e5c49 - End of configuration.
[testng] [2024-06-07 01:21:26,430] [pool-1-thread-10] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif:
[testng] 01:21:26,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:21:26,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:26,431 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-07_01-21-26.log]
[testng] 01:21:26,431 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d90592e - End of configuration.
[testng] [2024-06-07 01:21:26,473] [pool-1-thread-9] Initializing /data/samples/Leica_sample.lei:
[testng] 01:21:26,474 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:21:26,474 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:26,475 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-07_01-21-26.log]
[testng] 01:21:26,475 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25b9857a - End of configuration.
[testng] [2024-06-07 01:21:26,499] [pool-1-thread-8] Initializing /data/clay/leica_stack.lei:
[testng] 01:21:26,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:21:26,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:26,500 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-07_01-21-26.log]
[testng] 01:21:26,500 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6831da68 - End of configuration.
[testng] [2024-06-07 01:21:26,520] [pool-1-thread-7] Initializing /data/brian/leica-original/050118.lei:
[testng] 01:21:26,520 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:21:26,520 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:26,521 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-07_01-21-26.log]
[testng] 01:21:26,521 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ac08146 - End of configuration.
[testng] [2024-06-07 01:21:26,813] [pool-1-thread-6] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei:
[testng] 01:21:26,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:21:26,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:26,814 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-07_01-21-26.log]
[testng] 01:21:26,814 |-INFO in ch.qos.logback.core.sift.SiftProcessor@659f4cf8 - End of configuration.
[testng] [2024-06-07 01:21:26,856] [pool-1-thread-5] Initializing /data/julie/c164_1.tif:
[testng] 01:21:26,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:21:26,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:26,857 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-07_01-21-26.log]
[testng] 01:21:26,857 |-INFO in ch.qos.logback.core.sift.SiftProcessor@184d66b7 - End of configuration.
[testng] [2024-06-07 01:21:27,306] [pool-1-thread-4] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg:
[testng] 01:21:27,306 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:21:27,306 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:27,307 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-07_01-21-27.log]
[testng] 01:21:27,307 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f512ae4 - End of configuration.
[testng] [2024-06-07 01:21:27,314] [pool-1-thread-3] Initializing /data/david/megan/megan.lei:
[testng] 01:21:27,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:21:27,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:27,315 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-07_01-21-27.log]
[testng] 01:21:27,315 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25b02cbc - End of configuration.
[testng] [2024-06-07 01:21:27,365] [pool-1-thread-2] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei:
[testng] 01:21:27,365 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:21:27,365 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:21:27,365 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-07_01-21-27.log]
[testng] 01:21:27,366 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35ed1447 - End of configuration.
[testng] [2024-06-07 01:21:28,346] [pool-1-thread-12] Initializing /data/julie/biorad/8291mcd8_raw01.pic:
[testng] [2024-06-07 01:21:28,486] [pool-1-thread-4] Initializing /data/constantin/cell6/Graphs_1_00.jpg:
[testng] [2024-06-07 01:21:28,498] [pool-1-thread-9] Initializing /data/stjude/NIHSSE02-3.lei:
[testng] [2024-06-07 01:21:28,533] [pool-1-thread-2] Initializing /data/michael/2007-01-31_zres_sp2.lei:
[testng] [2024-06-07 01:21:28,576] [pool-1-thread-8] Initializing /data/constantin/cell6/Quant_Image_01.jpg:
[testng] [2024-06-07 01:21:28,710] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6.lei:
[testng] [2024-06-07 01:21:28,775] [pool-1-thread-8] Initializing /data/martin/samples-SP2/samples-SP2.lei:
[testng] [2024-06-07 01:21:28,913] [pool-1-thread-4] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei:
[testng] [2024-06-07 01:21:29,292] [pool-1-thread-12] Initializing /data/joel/sequential scan 3/sequential scan 3.lei:
[testng] [2024-06-07 01:21:29,541] [pool-1-thread-2] Initializing /data/simon/Leica demo/fish/fish.lei:
[testng] [2024-06-07 01:21:31,425] [pool-1-thread-5] Initializing /data/clay/leica_stack.tif:
[testng] [2024-06-07 01:21:31,724] [pool-1-thread-5] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei:
[testng] [2024-06-07 01:21:32,905] [pool-1-thread-9] Initializing /data/grant/Leica SP2 (25-11-10).lei:
[testng] [2024-06-07 01:21:39,881] [pool-1-thread-4] Initializing /data/brian/tropo/tropo.lei:
[testng] [2024-06-07 01:21:41,344] [pool-1-thread-4] Initializing /data/julie/biorad/25-65.tif:
[testng] [2024-06-07 01:21:42,051] [pool-1-thread-4] Initializing /data/david/intestine/intestine.lei:
[testng] [2024-06-07 01:21:44,858] [pool-1-thread-6] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg:
[testng] [2024-06-07 01:21:45,147] [pool-1-thread-6] Initializing /data/constantin/cell6/Logo.jpg:
[testng] [2024-06-07 01:21:45,275] [pool-1-thread-6] Initializing /data/andrey/10310500/10310500.lei:
[testng] [2024-06-07 01:21:46,206] [pool-1-thread-8] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei:
[testng] [2024-06-07 01:21:48,587] [pool-1-thread-10] Initializing /data/joel/sequential scan 2/sequential scan 2.lei:
[testng] [2024-06-07 01:21:48,895] [pool-1-thread-5] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei:
[testng] [2024-06-07 01:21:49,129] [pool-1-thread-1] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei:
[testng] [2024-06-07 01:21:51,220] [pool-1-thread-12] Initializing /data/vytas/4voxels/4voxels.lei:
[testng] [2024-06-07 01:21:51,637] [pool-1-thread-3] Initializing /data/christophe/Leica stacks/Nf5.lei:
[testng] [2024-06-07 01:21:55,109] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg:
[testng] [2024-06-07 01:21:55,223] [pool-1-thread-11] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei:
[testng] [2024-06-07 01:22:07,546] [pool-1-thread-3] Initializing /data/brian/050627-leica/050628-leica.lei:
[testng] [2024-06-07 01:22:08,234] [pool-1-thread-9] Initializing /data/constantin/cell6/Quant_Image_00.jpg:
[testng] [2024-06-07 01:22:08,348] [pool-1-thread-9] Initializing /data/constantin/cell6/cell6/Logo.jpg:
[testng] [2024-06-07 01:22:08,472] [pool-1-thread-9] Initializing /data/oliver/o459/o459.lei:
[testng] [2024-06-07 01:22:09,144] [pool-1-thread-10] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 2332, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 3 minutes 27 seconds
Finished: SUCCESS