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Started by upstream project "BIOFORMATS-test-repo" build number 214 originally caused by: Started by upstream project "Trigger" build number 241 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/jenkins15795334432288744090.sh + '[' leica = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_33927_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] 08:43:06,426 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 08:43:06,427 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 08:43:06,427 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 08:43:06,428 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 08:43:06,429 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 08:43:06,429 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 08:43:06,429 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 08:43:06,429 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 08:43:06,430 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 08:43:06,430 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 08:43:06,431 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 08:43:06,431 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 08:43:06,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 08:43:06,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 08:43:06,625 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 08:43:06,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 08:43:06,631 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 08:43:06,631 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 08:43:06,632 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 08:43:06,632 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 08:43:06,632 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 08:43:06,633 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 08:43:06,633 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 203 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-08 08:43:06,642] [main] java.version = 11.0.16 [testng] 08:43:06,645 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 08:43:06,645 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:43:06,687 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-08_08-43-06.log] [testng] 08:43:06,689 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-10-08 08:43:06,691] [main] testng.directory = /data [testng] [2024-10-08 08:43:06,691] [main] testng.configDirectory = /config [testng] [2024-10-08 08:43:06,700] [main] testng.multiplier = 1.0 [testng] [2024-10-08 08:43:06,702] [main] testng.in-memory = false [testng] [2024-10-08 08:43:06,702] [main] testng.allow-missing = false [testng] [2024-10-08 08:43:06,702] [main] user.language = en [testng] [2024-10-08 08:43:06,702] [main] user.country = ${user.country} [testng] [2024-10-08 08:43:06,702] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-08 08:43:42,038] [main] ---------------------------------------- [testng] [2024-10-08 08:43:42,038] [main] Total files: 5651 [testng] [2024-10-08 08:43:42,039] [main] Scan time: 35.336 s (6 ms/file) [testng] [2024-10-08 08:43:42,039] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-08 08:44:39,276] [pool-1-thread-1] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] 08:44:39,276 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 08:44:39,276 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:44:39,278 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-08_08-44-39.log] [testng] 08:44:39,278 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b532e62 - End of configuration. [testng] [2024-10-08 08:44:39,622] [pool-1-thread-12] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] 08:44:39,622 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 08:44:39,622 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:44:39,623 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-08_08-44-39.log] [testng] 08:44:39,623 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ec2045a - End of configuration. [testng] [2024-10-08 08:44:39,839] [pool-1-thread-11] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] 08:44:39,840 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 08:44:39,840 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:44:39,840 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-08_08-44-39.log] [testng] 08:44:39,841 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49012c5d - End of configuration. [testng] [2024-10-08 08:44:40,050] [pool-1-thread-10] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] 08:44:40,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 08:44:40,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:44:40,051 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-08_08-44-40.log] [testng] 08:44:40,051 |-INFO in ch.qos.logback.core.sift.SiftProcessor@689fb6da - End of configuration. [testng] [2024-10-08 08:44:40,331] [pool-1-thread-9] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] 08:44:40,331 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 08:44:40,331 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:44:40,332 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-08_08-44-40.log] [testng] 08:44:40,333 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6de4dbab - End of configuration. [testng] [2024-10-08 08:44:40,359] [pool-1-thread-8] Initializing /data/constantin/cell6/Logo.jpg: [testng] 08:44:40,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 08:44:40,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:44:40,360 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-08_08-44-40.log] [testng] 08:44:40,361 |-INFO in ch.qos.logback.core.sift.SiftProcessor@679b566b - End of configuration. [testng] [2024-10-08 08:44:40,383] [pool-1-thread-7] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] 08:44:40,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 08:44:40,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:44:40,384 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-08_08-44-40.log] [testng] 08:44:40,384 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a5e3fe4 - End of configuration. [testng] [2024-10-08 08:44:41,030] [pool-1-thread-6] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] 08:44:41,030 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 08:44:41,030 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:44:41,031 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-08_08-44-41.log] [testng] 08:44:41,031 |-INFO in ch.qos.logback.core.sift.SiftProcessor@96e3986 - End of configuration. [testng] [2024-10-08 08:44:41,178] [pool-1-thread-5] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] 08:44:41,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 08:44:41,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:44:41,179 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-08_08-44-41.log] [testng] 08:44:41,179 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61c0122f - End of configuration. [testng] [2024-10-08 08:44:41,449] [pool-1-thread-4] Initializing /data/brian/leica-original/050118.lei: [testng] 08:44:41,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 08:44:41,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:44:41,450 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-08_08-44-41.log] [testng] 08:44:41,450 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26c6b760 - End of configuration. [testng] [2024-10-08 08:44:42,411] [pool-1-thread-3] Initializing /data/oliver/o459/o459.lei: [testng] 08:44:42,411 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 08:44:42,411 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:44:42,411 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-08_08-44-42.log] [testng] 08:44:42,412 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b50939d - End of configuration. [testng] [2024-10-08 08:44:42,968] [pool-1-thread-2] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] 08:44:42,969 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 08:44:42,969 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:44:42,969 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-08_08-44-42.log] [testng] 08:44:42,969 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29375782 - End of configuration. [testng] [2024-10-08 08:44:45,647] [pool-1-thread-2] Initializing /data/constantin/cell6/cell6.lei: [testng] [2024-10-08 08:44:46,401] [pool-1-thread-8] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2024-10-08 08:44:47,163] [pool-1-thread-9] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-10-08 08:44:54,162] [pool-1-thread-6] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-10-08 08:47:56,832] [pool-1-thread-5] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-10-08 08:48:51,910] [pool-1-thread-11] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2024-10-08 08:48:59,749] [pool-1-thread-11] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] [2024-10-08 08:49:16,248] [pool-1-thread-11] Initializing /data/brian/tropo/tropo.lei: [testng] [2024-10-08 08:49:34,401] [pool-1-thread-11] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] [2024-10-08 08:49:37,270] [pool-1-thread-11] Initializing /data/julie/biorad/25-65.tif: [testng] [2024-10-08 08:49:42,854] [pool-1-thread-11] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2024-10-08 08:49:48,796] [pool-1-thread-11] Initializing /data/clay/leica_stack.lei: [testng] [2024-10-08 08:50:04,270] [pool-1-thread-11] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] [2024-10-08 08:50:06,326] [pool-1-thread-11] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2024-10-08 08:50:07,353] [pool-1-thread-12] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [2024-10-08 08:50:10,133] [pool-1-thread-12] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] [2024-10-08 08:50:58,326] [pool-1-thread-10] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2024-10-08 08:51:05,716] [pool-1-thread-2] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2024-10-08 08:51:11,745] [pool-1-thread-8] Initializing /data/clay/leica_stack.tif: [testng] [2024-10-08 08:51:15,981] [pool-1-thread-8] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-10-08 08:52:40,168] [pool-1-thread-12] Initializing /data/david/megan/megan.lei: [testng] [2024-10-08 08:53:09,104] [pool-1-thread-10] Initializing /data/samples/Leica_sample.lei: [testng] [2024-10-08 08:53:10,686] [pool-1-thread-1] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2024-10-08 08:53:16,489] [pool-1-thread-10] Initializing /data/julie/c164_1.tif: [testng] [2024-10-08 08:53:26,680] [pool-1-thread-10] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] [2024-10-08 08:53:41,909] [pool-1-thread-10] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2024-10-08 08:53:50,915] [pool-1-thread-4] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] [2024-10-08 08:53:53,669] [pool-1-thread-4] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2024-10-08 08:53:57,434] [pool-1-thread-8] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2024-10-08 08:53:59,614] [pool-1-thread-8] Initializing /data/david/intestine/intestine.lei: [testng] [2024-10-08 08:54:10,521] [pool-1-thread-1] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-10-08 08:54:13,419] [pool-1-thread-1] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] 09:49:04,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 09:49:04,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:49:04,789 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-08_09-49-04.log] [testng] 09:49:04,790 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19542115 - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2332, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 66 minutes 1 second Finished: SUCCESS