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Started by upstream project "BIOFORMATS-test-repo" build number 38 originally caused by: Started by upstream project "Trigger" build number 44 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/jenkins17360963711604183657.sh + '[' leica = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_5219_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] 09:05:06,312 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 09:05:06,314 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 09:05:06,314 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:05:06,315 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:05:06,315 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 09:05:06,315 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 09:05:06,316 |-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] 09:05:06,316 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:05:06,316 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:05:06,316 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 09:05:06,316 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 09:05:06,316 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 09:05:06,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 09:05:06,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 09:05:06,552 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 09:05:06,552 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 09:05:06,566 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 09:05:06,566 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 09:05:06,566 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 09:05:06,567 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 09:05:06,567 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 09:05:06,568 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 09:05:06,568 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 252 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-19 09:05:06,577] [main] java.version = 1.8.0_342 [testng] 09:05:06,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 09:05:06,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:05:06,626 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-19_09-05-06.log] [testng] 09:05:06,627 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-04-19 09:05:06,629] [main] testng.directory = /data [testng] [2024-04-19 09:05:06,630] [main] testng.configDirectory = /config [testng] [2024-04-19 09:05:06,641] [main] testng.multiplier = 1.0 [testng] [2024-04-19 09:05:06,641] [main] testng.in-memory = false [testng] [2024-04-19 09:05:06,641] [main] testng.allow-missing = false [testng] [2024-04-19 09:05:06,641] [main] user.language = en [testng] [2024-04-19 09:05:06,641] [main] user.country = ${user.country} [testng] [2024-04-19 09:05:06,642] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-04-19 09:05:18,244] [main] ---------------------------------------- [testng] [2024-04-19 09:05:18,245] [main] Total files: 5651 [testng] [2024-04-19 09:05:18,245] [main] Scan time: 11.602 s (2 ms/file) [testng] [2024-04-19 09:05:18,245] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-19 09:05:35,000] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6.lei: [testng] 09:05:35,001 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 09:05:35,001 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:05:35,002 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-19_09-05-35.log] [testng] 09:05:35,003 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5485eca4 - End of configuration. [testng] [2024-04-19 09:05:35,078] [pool-1-thread-12] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] 09:05:35,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 09:05:35,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:05:35,079 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-19_09-05-35.log] [testng] 09:05:35,080 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7136f4b9 - End of configuration. [testng] [2024-04-19 09:05:35,140] [pool-1-thread-11] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] 09:05:35,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 09:05:35,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:05:35,141 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-19_09-05-35.log] [testng] 09:05:35,141 |-INFO in ch.qos.logback.core.sift.SiftProcessor@685f5cbf - End of configuration. [testng] [2024-04-19 09:05:35,323] [pool-1-thread-10] Initializing /data/julie/biorad/25-65.tif: [testng] 09:05:35,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 09:05:35,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:05:35,324 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-19_09-05-35.log] [testng] 09:05:35,325 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b5572f0 - End of configuration. [testng] [2024-04-19 09:05:35,363] [pool-1-thread-9] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] 09:05:35,364 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 09:05:35,364 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:05:35,364 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-19_09-05-35.log] [testng] 09:05:35,365 |-INFO in ch.qos.logback.core.sift.SiftProcessor@572bb104 - End of configuration. [testng] [2024-04-19 09:05:35,472] [pool-1-thread-8] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] 09:05:35,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 09:05:35,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:05:35,473 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-19_09-05-35.log] [testng] 09:05:35,473 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2554a9ca - End of configuration. [testng] [2024-04-19 09:05:35,503] [pool-1-thread-7] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] 09:05:35,504 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 09:05:35,504 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:05:35,504 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-19_09-05-35.log] [testng] 09:05:35,505 |-INFO in ch.qos.logback.core.sift.SiftProcessor@389d2bf6 - End of configuration. [testng] [2024-04-19 09:05:35,511] [pool-1-thread-6] Initializing /data/clay/leica_stack.lei: [testng] 09:05:35,512 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 09:05:35,512 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:05:35,513 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-19_09-05-35.log] [testng] 09:05:35,513 |-INFO in ch.qos.logback.core.sift.SiftProcessor@765c7849 - End of configuration. [testng] [2024-04-19 09:05:35,551] [pool-1-thread-5] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] 09:05:35,551 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 09:05:35,551 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:05:35,551 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-19_09-05-35.log] [testng] 09:05:35,552 |-INFO in ch.qos.logback.core.sift.SiftProcessor@468bf7ac - End of configuration. [testng] [2024-04-19 09:05:35,624] [pool-1-thread-4] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] 09:05:35,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 09:05:35,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:05:35,625 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-19_09-05-35.log] [testng] 09:05:35,625 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61db4237 - End of configuration. [testng] [2024-04-19 09:05:35,652] [pool-1-thread-3] Initializing /data/andrey/10310500/10310500.lei: [testng] 09:05:35,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 09:05:35,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:05:35,654 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-19_09-05-35.log] [testng] 09:05:35,655 |-INFO in ch.qos.logback.core.sift.SiftProcessor@400ff76a - End of configuration. [testng] [2024-04-19 09:05:35,772] [pool-1-thread-2] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] 09:05:35,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 09:05:35,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:05:35,773 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-19_09-05-35.log] [testng] 09:05:35,774 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c21a385 - End of configuration. [testng] [2024-04-19 09:05:37,346] [pool-1-thread-4] Initializing /data/oliver/o459/o459.lei: [testng] [2024-04-19 09:05:37,491] [pool-1-thread-7] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2024-04-19 09:05:37,534] [pool-1-thread-6] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2024-04-19 09:05:37,721] [pool-1-thread-10] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2024-04-19 09:05:37,816] [pool-1-thread-8] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2024-04-19 09:05:38,182] [pool-1-thread-8] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2024-04-19 09:05:38,991] [pool-1-thread-7] Initializing /data/brian/leica-original/050118.lei: [testng] [2024-04-19 09:05:43,771] [pool-1-thread-10] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2024-04-19 09:05:51,393] [pool-1-thread-12] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2024-04-19 09:05:51,585] [pool-1-thread-8] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-04-19 09:05:51,728] [pool-1-thread-5] Initializing /data/david/megan/megan.lei: [testng] [2024-04-19 09:05:51,969] [pool-1-thread-8] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2024-04-19 09:05:52,075] [pool-1-thread-8] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2024-04-19 09:05:52,689] [pool-1-thread-12] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2024-04-19 09:05:53,542] [pool-1-thread-1] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-04-19 09:05:56,371] [pool-1-thread-11] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-04-19 09:06:01,239] [pool-1-thread-10] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] [2024-04-19 09:06:01,399] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2024-04-19 09:06:01,555] [pool-1-thread-10] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-04-19 09:06:01,707] [pool-1-thread-10] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] [2024-04-19 09:06:02,272] [pool-1-thread-10] Initializing /data/brian/tropo/tropo.lei: [testng] [2024-04-19 09:06:03,195] [pool-1-thread-6] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] [2024-04-19 09:06:03,425] [pool-1-thread-6] Initializing /data/david/intestine/intestine.lei: [testng] [2024-04-19 09:06:04,139] [pool-1-thread-10] Initializing /data/julie/c164_1.tif: [testng] [2024-04-19 09:06:09,780] [pool-1-thread-10] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] [2024-04-19 09:06:10,928] [pool-1-thread-10] Initializing /data/clay/leica_stack.tif: [testng] [2024-04-19 09:06:11,205] [pool-1-thread-10] Initializing /data/samples/Leica_sample.lei: [testng] [2024-04-19 09:06:11,613] [pool-1-thread-10] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2024-04-19 09:06:13,521] [pool-1-thread-5] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2024-04-19 09:06:15,463] [pool-1-thread-9] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2024-04-19 09:06:20,668] [pool-1-thread-1] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2024-04-19 09:06:21,137] [pool-1-thread-4] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [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