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Started by upstream project "BIOFORMATS-test-repo" build number 215 originally caused by: Started by upstream project "Trigger" build number 242 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/jenkins852428501315048199.sh + '[' leica = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_34038_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] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 01:20:56,484 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:20:56,485 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 01:20:56,485 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:20:56,486 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:20:56,487 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:20:56,487 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:20:56,487 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:20:56,487 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:20:56,488 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:20:56,488 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:20:56,489 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:20:56,489 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:20:56,692 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:20:56,692 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:20:56,713 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:20:56,713 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:20:56,718 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:20:56,718 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:20:56,718 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:20:56,718 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:20:56,718 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 01:20:56,719 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 01:20:56,720 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 232 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-09 01:20:56,728] [main] java.version = 17.0.2 [testng] 01:20:56,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:20:56,731 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:56,769 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-09_01-20-56.log] [testng] 01:20:56,770 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-10-09 01:20:56,772] [main] testng.directory = /data [testng] [2024-10-09 01:20:56,772] [main] testng.configDirectory = /config [testng] [2024-10-09 01:20:56,780] [main] testng.multiplier = 1.0 [testng] [2024-10-09 01:20:56,781] [main] testng.in-memory = false [testng] [2024-10-09 01:20:56,781] [main] testng.allow-missing = false [testng] [2024-10-09 01:20:56,781] [main] user.language = en [testng] [2024-10-09 01:20:56,781] [main] user.country = ${user.country} [testng] [2024-10-09 01:20:56,781] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-09 01:21:08,550] [main] ---------------------------------------- [testng] [2024-10-09 01:21:08,550] [main] Total files: 5651 [testng] [2024-10-09 01:21:08,551] [main] Scan time: 11.769 s (2 ms/file) [testng] [2024-10-09 01:21:08,551] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-09 01:21:33,104] [pool-1-thread-1] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] 01:21:33,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:21:33,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:33,105 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-09_01-21-33.log] [testng] 01:21:33,106 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4548f3e0 - End of configuration. [testng] [2024-10-09 01:21:33,309] [pool-1-thread-12] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] 01:21:33,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:21:33,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:33,310 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-09_01-21-33.log] [testng] 01:21:33,310 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34b50692 - End of configuration. [testng] [2024-10-09 01:21:33,513] [pool-1-thread-11] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] 01:21:33,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:21:33,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:33,514 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-09_01-21-33.log] [testng] 01:21:33,515 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d77b79 - End of configuration. [testng] [2024-10-09 01:21:33,757] [pool-1-thread-10] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] 01:21:33,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:21:33,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:33,758 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-09_01-21-33.log] [testng] 01:21:33,758 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15f9ef41 - End of configuration. [testng] [2024-10-09 01:21:34,033] [pool-1-thread-9] Initializing /data/clay/leica_stack.lei: [testng] 01:21:34,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:21:34,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:34,034 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-09_01-21-34.log] [testng] 01:21:34,034 |-INFO in ch.qos.logback.core.sift.SiftProcessor@88fdff4 - End of configuration. [testng] [2024-10-09 01:21:34,243] [pool-1-thread-8] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] 01:21:34,243 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:21:34,243 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:34,244 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-09_01-21-34.log] [testng] 01:21:34,244 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65667a9d - End of configuration. [testng] [2024-10-09 01:21:34,696] [pool-1-thread-7] Initializing /data/david/megan/megan.lei: [testng] 01:21:34,696 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:21:34,697 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:34,697 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-09_01-21-34.log] [testng] 01:21:34,698 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56678ad2 - End of configuration. [testng] [2024-10-09 01:21:34,963] [pool-1-thread-6] Initializing /data/julie/biorad/25-65.tif: [testng] 01:21:34,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:21:34,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:34,964 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-09_01-21-34.log] [testng] 01:21:34,964 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4795ddfe - End of configuration. [testng] [2024-10-09 01:21:35,423] [pool-1-thread-5] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] 01:21:35,423 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:21:35,423 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:35,424 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-09_01-21-35.log] [testng] 01:21:35,424 |-INFO in ch.qos.logback.core.sift.SiftProcessor@510fc080 - End of configuration. [testng] [2024-10-09 01:21:35,467] [pool-1-thread-4] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] 01:21:35,467 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:21:35,467 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:35,468 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-09_01-21-35.log] [testng] 01:21:35,468 |-INFO in ch.qos.logback.core.sift.SiftProcessor@157e062c - End of configuration. [testng] [2024-10-09 01:21:35,511] [pool-1-thread-3] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] 01:21:35,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:21:35,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:35,512 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-09_01-21-35.log] [testng] 01:21:35,512 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f303632 - End of configuration. [testng] [2024-10-09 01:21:35,894] [pool-1-thread-2] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] 01:21:35,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:21:35,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:35,895 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-09_01-21-35.log] [testng] 01:21:35,896 |-INFO in ch.qos.logback.core.sift.SiftProcessor@274504df - End of configuration. [testng] [2024-10-09 01:21:38,740] [pool-1-thread-5] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-10-09 01:21:38,842] [pool-1-thread-4] Initializing /data/oliver/o459/o459.lei: [testng] [2024-10-09 01:21:41,861] [pool-1-thread-5] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2024-10-09 01:21:42,742] [pool-1-thread-6] Initializing /data/julie/c164_1.tif: [testng] [2024-10-09 01:21:51,307] [pool-1-thread-12] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-10-09 01:21:52,644] [pool-1-thread-9] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2024-10-09 01:21:53,471] [pool-1-thread-6] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-10-09 01:21:56,885] [pool-1-thread-6] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2024-10-09 01:21:59,431] [pool-1-thread-2] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2024-10-09 01:22:01,329] [pool-1-thread-6] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-10-09 01:24:11,144] [pool-1-thread-11] Initializing /data/david/intestine/intestine.lei: [testng] [2024-10-09 01:24:24,115] [pool-1-thread-9] Initializing /data/constantin/cell6/cell6.lei: [testng] [2024-10-09 01:24:33,380] [pool-1-thread-3] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2024-10-09 01:24:57,417] [pool-1-thread-12] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2024-10-09 01:26:47,496] [pool-1-thread-10] Initializing /data/samples/Leica_sample.lei: [testng] [2024-10-09 01:27:00,543] [pool-1-thread-10] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2024-10-09 01:27:43,048] [pool-1-thread-1] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-10-09 01:28:13,399] [pool-1-thread-7] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2024-10-09 01:29:18,549] [pool-1-thread-2] Initializing /data/brian/tropo/tropo.lei: [testng] [2024-10-09 01:29:25,142] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2024-10-09 01:29:27,044] [pool-1-thread-11] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2024-10-09 01:29:32,174] [pool-1-thread-5] Initializing /data/clay/leica_stack.tif: [testng] [2024-10-09 01:29:34,966] [pool-1-thread-2] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2024-10-09 01:29:36,897] [pool-1-thread-5] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] [2024-10-09 01:29:39,534] [pool-1-thread-9] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2024-10-09 01:29:44,998] [pool-1-thread-9] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2024-10-09 01:29:45,229] [pool-1-thread-5] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2024-10-09 01:29:46,704] [pool-1-thread-9] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2024-10-09 01:29:50,535] [pool-1-thread-5] Initializing /data/brian/leica-original/050118.lei: [testng] [2024-10-09 01:30:05,810] [pool-1-thread-12] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-10-09 01:30:16,744] [pool-1-thread-11] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] [2024-10-09 01:30:19,268] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2332, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 47 minutes 40 seconds Finished: SUCCESS