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Started by upstream project "BIOFORMATS-test-repo" build number 12 originally caused by: Started by upstream project "Trigger" build number 15 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/jenkins5386634663958003636.sh + '[' leica = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_1773_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 [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] 1 warning test-automated: [testng] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 00:19:59,066 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:19:59,067 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 00:19:59,067 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:19:59,068 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:19:59,068 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:19:59,069 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:19:59,069 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:19:59,069 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:19:59,070 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:19:59,070 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:19:59,070 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:19:59,071 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:19:59,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:19:59,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:19:59,261 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:19:59,261 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:19:59,267 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:19:59,267 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:19:59,267 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:19:59,267 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:19:59,267 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 00:19:59,268 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 00:19:59,269 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 199 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-26 00:19:59,277] [main] java.version = 11.0.16 [testng] 00:19:59,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:19:59,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:19:59,323 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-26_00-19-59.log] [testng] 00:19:59,325 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-03-26 00:19:59,327] [main] testng.directory = /data [testng] [2024-03-26 00:19:59,327] [main] testng.configDirectory = /config [testng] [2024-03-26 00:19:59,337] [main] testng.multiplier = 1.0 [testng] [2024-03-26 00:19:59,338] [main] testng.in-memory = false [testng] [2024-03-26 00:19:59,338] [main] testng.allow-missing = false [testng] [2024-03-26 00:19:59,338] [main] user.language = en [testng] [2024-03-26 00:19:59,338] [main] user.country = ${user.country} [testng] [2024-03-26 00:19:59,338] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-26 00:20:11,495] [main] ---------------------------------------- [testng] [2024-03-26 00:20:11,496] [main] Total files: 5651 [testng] [2024-03-26 00:20:11,496] [main] Scan time: 12.157 s (2 ms/file) [testng] [2024-03-26 00:20:11,496] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-26 00:20:35,369] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] 00:20:35,370 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:20:35,370 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:35,372 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-26_00-20-35.log] [testng] 00:20:35,372 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f07696e - End of configuration. [testng] [2024-03-26 00:20:35,452] [pool-1-thread-12] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] 00:20:35,452 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:20:35,452 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:35,453 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-26_00-20-35.log] [testng] 00:20:35,454 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44dafc59 - End of configuration. [testng] [2024-03-26 00:20:35,499] [pool-1-thread-11] Initializing /data/clay/leica_stack.lei: [testng] 00:20:35,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:20:35,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:35,500 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-26_00-20-35.log] [testng] 00:20:35,500 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15ce766a - End of configuration. [testng] [2024-03-26 00:20:35,549] [pool-1-thread-10] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] 00:20:35,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:20:35,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:35,550 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-26_00-20-35.log] [testng] 00:20:35,550 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5698c082 - End of configuration. [testng] [2024-03-26 00:20:35,675] [pool-1-thread-9] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] 00:20:35,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:20:35,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:35,676 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-26_00-20-35.log] [testng] 00:20:35,677 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65de311b - End of configuration. [testng] [2024-03-26 00:20:35,692] [pool-1-thread-8] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] 00:20:35,692 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:20:35,692 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:35,693 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-26_00-20-35.log] [testng] 00:20:35,694 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3192bc23 - End of configuration. [testng] [2024-03-26 00:20:35,752] [pool-1-thread-7] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] 00:20:35,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:20:35,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:35,753 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-26_00-20-35.log] [testng] 00:20:35,754 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6de4dbab - End of configuration. [testng] [2024-03-26 00:20:36,034] [pool-1-thread-6] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] 00:20:36,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:20:36,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:36,035 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-26_00-20-36.log] [testng] 00:20:36,035 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ba7ba8c - End of configuration. [testng] [2024-03-26 00:20:36,668] [pool-1-thread-5] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] 00:20:36,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:20:36,669 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:36,669 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-26_00-20-36.log] [testng] 00:20:36,670 |-INFO in ch.qos.logback.core.sift.SiftProcessor@121a7e8 - End of configuration. [testng] [2024-03-26 00:20:36,846] [pool-1-thread-4] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] 00:20:36,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:20:36,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:36,847 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-26_00-20-36.log] [testng] 00:20:36,847 |-INFO in ch.qos.logback.core.sift.SiftProcessor@661bab52 - End of configuration. [testng] [2024-03-26 00:20:36,961] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6.lei: [testng] 00:20:36,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:20:36,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:36,962 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-26_00-20-36.log] [testng] 00:20:36,963 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56b5526a - End of configuration. [testng] [2024-03-26 00:20:37,069] [pool-1-thread-2] Initializing /data/samples/Leica_sample.lei: [testng] 00:20:37,069 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:20:37,069 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:37,070 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-26_00-20-37.log] [testng] 00:20:37,070 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6972623 - End of configuration. [testng] [2024-03-26 00:20:38,752] [pool-1-thread-9] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2024-03-26 00:20:38,937] [pool-1-thread-12] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-03-26 00:20:39,154] [pool-1-thread-1] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-03-26 00:20:40,241] [pool-1-thread-2] Initializing /data/david/intestine/intestine.lei: [testng] [2024-03-26 00:20:41,556] [pool-1-thread-11] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] [2024-03-26 00:20:42,396] [pool-1-thread-11] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] [2024-03-26 00:20:47,929] [pool-1-thread-11] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2024-03-26 00:20:57,944] [pool-1-thread-9] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2024-03-26 00:21:00,680] [pool-1-thread-9] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] [2024-03-26 00:21:02,974] [pool-1-thread-9] testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile) [testng] [2024-03-26 00:21:03,567] [pool-1-thread-9] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] [2024-03-26 00:21:08,210] [pool-1-thread-9] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] [2024-03-26 00:21:29,126] [pool-1-thread-10] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2024-03-26 00:22:04,966] [pool-1-thread-8] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-03-26 00:22:05,688] [pool-1-thread-8] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-03-26 00:22:24,875] [pool-1-thread-3] Initializing /data/david/megan/megan.lei: [testng] [2024-03-26 00:22:26,556] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2024-03-26 00:22:27,913] [pool-1-thread-10] Initializing /data/clay/leica_stack.tif: [testng] [2024-03-26 00:22:30,148] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [2024-03-26 00:22:31,140] [pool-1-thread-10] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2024-03-26 00:22:32,436] [pool-1-thread-4] Initializing /data/julie/c164_1.tif: [testng] [2024-03-26 00:22:39,273] [pool-1-thread-4] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2024-03-26 00:22:48,487] [pool-1-thread-11] Initializing /data/julie/biorad/25-65.tif: [testng] [2024-03-26 00:22:49,153] [pool-1-thread-2] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-03-26 00:22:51,268] [pool-1-thread-11] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] [2024-03-26 00:22:52,165] [pool-1-thread-11] Initializing /data/brian/tropo/tropo.lei: [testng] [2024-03-26 00:22:58,694] [pool-1-thread-11] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2024-03-26 00:23:00,451] [pool-1-thread-9] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-03-26 00:23:01,276] [pool-1-thread-9] Initializing /data/oliver/o459/o459.lei: [testng] [2024-03-26 00:23:13,901] [pool-1-thread-8] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2024-03-26 00:23:16,291] [pool-1-thread-1] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2024-03-26 00:23:19,018] [pool-1-thread-10] Initializing /data/brian/leica-original/050118.lei: [testng] [2024-03-26 00:23:26,606] [pool-1-thread-5] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2332, Failures: 1, Skips: 0 [testng] =============================================== [testng] [testng] The tests failed. BUILD FAILED /bio-formats-build/bioformats/components/test-suite/build.xml:270: if=failedTest Total time: 10 minutes 32 seconds Build step 'Execute shell' marked build as failure Finished: FAILURE