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Started by upstream project "BIOFORMATS-test-repo" build number 183 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/jenkins14579441610847113617.sh + '[' leica = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_28843_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] 12:20:41,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 12:20:41,914 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 12:20:41,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 12:20:41,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 12:20:41,974 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 12:20:41,974 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 12:20:41,974 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 12:20:41,975 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 12:20:41,975 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@41a0aa7d - End of configuration. [testng] 12:20:41,975 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6574a52c - Registering current configuration as safe fallback point [testng] 12:20:41,976 |-INFO in ch.qos.logback.classic.util.ContextInitializer@6c1a5b54 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 471 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-10 12:20:41,985] [main] java.version = 11.0.16 [testng] 12:20:41,989 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 12:20:41,989 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:20:42,284 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-10_12-20-42.log] [testng] 12:20:42,285 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-09-10 12:20:42,323] [main] testng.directory = /data [testng] [2024-09-10 12:20:42,323] [main] testng.configDirectory = /config [testng] [2024-09-10 12:20:42,420] [main] testng.multiplier = 1.0 [testng] [2024-09-10 12:20:42,421] [main] testng.in-memory = false [testng] [2024-09-10 12:20:42,422] [main] testng.allow-missing = false [testng] [2024-09-10 12:20:42,422] [main] user.language = en [testng] [2024-09-10 12:20:42,422] [main] user.country = ${user.country} [testng] [2024-09-10 12:20:42,422] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-09-10 12:21:00,210] [main] ---------------------------------------- [testng] [2024-09-10 12:21:00,210] [main] Total files: 5651 [testng] [2024-09-10 12:21:00,211] [main] Scan time: 17.788 s (3 ms/file) [testng] [2024-09-10 12:21:00,211] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-10 12:21:18,984] [pool-1-thread-1] Initializing /data/brian/leica-original/050118.lei: [testng] 12:21:18,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 12:21:18,986 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:21:18,992 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-10_12-21-18.log] [testng] 12:21:18,993 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53e4cc93 - End of configuration. [testng] [2024-09-10 12:21:19,650] [pool-1-thread-12] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] 12:21:19,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 12:21:19,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:21:19,652 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-10_12-21-19.log] [testng] 12:21:19,652 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fde64d8 - End of configuration. [testng] [2024-09-10 12:21:19,912] [pool-1-thread-11] Initializing /data/oliver/o459/o459.lei: [testng] 12:21:19,912 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 12:21:19,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:21:19,913 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-10_12-21-19.log] [testng] 12:21:19,914 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73cb471b - End of configuration. [testng] [2024-09-10 12:21:20,086] [pool-1-thread-10] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] 12:21:20,086 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 12:21:20,086 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:21:20,087 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-10_12-21-20.log] [testng] 12:21:20,088 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7577ef5a - End of configuration. [testng] [2024-09-10 12:21:20,180] [pool-1-thread-9] Initializing /data/constantin/cell6/cell6.lei: [testng] 12:21:20,180 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 12:21:20,180 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:21:20,182 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-10_12-21-20.log] [testng] 12:21:20,182 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75574f11 - End of configuration. [testng] [2024-09-10 12:21:20,265] [pool-1-thread-8] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] 12:21:20,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 12:21:20,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:21:20,267 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-10_12-21-20.log] [testng] 12:21:20,267 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a11cb47 - End of configuration. [testng] [2024-09-10 12:21:20,295] [pool-1-thread-7] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] 12:21:20,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 12:21:20,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:21:20,296 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-10_12-21-20.log] [testng] 12:21:20,297 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4eb516c3 - End of configuration. [testng] [2024-09-10 12:21:20,347] [pool-1-thread-6] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] 12:21:20,347 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 12:21:20,347 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:21:20,348 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-10_12-21-20.log] [testng] 12:21:20,349 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22d3dcc2 - End of configuration. [testng] [2024-09-10 12:21:20,557] [pool-1-thread-5] Initializing /data/clay/leica_stack.lei: [testng] 12:21:20,557 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 12:21:20,558 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:21:20,559 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-10_12-21-20.log] [testng] 12:21:20,560 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11cc469e - End of configuration. [testng] [2024-09-10 12:21:20,608] [pool-1-thread-4] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] 12:21:20,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 12:21:20,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:21:20,609 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-10_12-21-20.log] [testng] 12:21:20,610 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51c43672 - End of configuration. [testng] [2024-09-10 12:21:20,664] [pool-1-thread-3] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] 12:21:20,665 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 12:21:20,665 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:21:20,665 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-10_12-21-20.log] [testng] 12:21:20,666 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ecb6e05 - End of configuration. [testng] [2024-09-10 12:21:20,721] [pool-1-thread-2] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] 12:21:20,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 12:21:20,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:21:20,723 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-10_12-21-20.log] [testng] 12:21:20,723 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ff42224 - End of configuration. [testng] [2024-09-10 12:21:21,878] [pool-1-thread-8] Initializing /data/david/megan/megan.lei: [testng] [2024-09-10 12:21:21,977] [pool-1-thread-2] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2024-09-10 12:21:23,441] [pool-1-thread-5] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] [2024-09-10 12:21:23,961] [pool-1-thread-10] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2024-09-10 12:21:25,434] [pool-1-thread-5] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2024-09-10 12:21:41,282] [pool-1-thread-4] Initializing /data/samples/Leica_sample.lei: [testng] [2024-09-10 12:21:42,530] [pool-1-thread-4] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2024-09-10 12:21:44,690] [pool-1-thread-4] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-09-10 12:21:45,967] [pool-1-thread-7] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2024-09-10 12:21:46,194] [pool-1-thread-5] Initializing /data/julie/c164_1.tif: [testng] [2024-09-10 12:21:46,708] [pool-1-thread-7] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] [2024-09-10 12:21:47,552] [pool-1-thread-12] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-09-10 12:21:47,621] [pool-1-thread-7] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] [2024-09-10 12:21:47,861] [pool-1-thread-7] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] [2024-09-10 12:21:48,178] [pool-1-thread-12] Initializing /data/david/intestine/intestine.lei: [testng] [2024-09-10 12:21:50,736] [pool-1-thread-3] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2024-09-10 12:21:51,031] [pool-1-thread-5] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2024-09-10 12:21:52,251] [pool-1-thread-5] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2024-09-10 12:21:54,215] [pool-1-thread-9] Initializing /data/brian/tropo/tropo.lei: [testng] [2024-09-10 12:21:56,324] [pool-1-thread-9] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-09-10 12:21:56,504] [pool-1-thread-9] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2024-09-10 12:21:57,604] [pool-1-thread-10] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2024-09-10 12:21:59,513] [pool-1-thread-6] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-09-10 12:22:00,810] [pool-1-thread-8] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2024-09-10 12:22:14,363] [pool-1-thread-7] Initializing /data/clay/leica_stack.tif: [testng] [2024-09-10 12:22:14,866] [pool-1-thread-7] Initializing /data/julie/biorad/25-65.tif: [testng] [2024-09-10 12:22:15,833] [pool-1-thread-7] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2024-09-10 12:22:16,038] [pool-1-thread-7] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-09-10 12:22:25,766] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2024-09-10 12:22:25,964] [pool-1-thread-10] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-09-10 12:22:27,855] [pool-1-thread-3] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] [2024-09-10 12:22:28,044] [pool-1-thread-3] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2332, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 5 minutes 20 seconds Finished: SUCCESS