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Started by upstream project "BIOFORMATS-test-repo" build number 219 originally caused by: Started by upstream project "Trigger" build number 246 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/jenkins11229662948998302664.sh + '[' leica = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_34695_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] 01:20:13,374 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:20:13,375 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 01:20:13,375 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:20:13,376 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:20:13,376 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:20:13,377 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:20:13,377 |-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] 01:20:13,377 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:20:13,377 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:20:13,378 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:20:13,378 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:20:13,378 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:20:13,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:20:13,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:20:13,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:20:13,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:20:13,572 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:20:13,572 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:20:13,572 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:20:13,572 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:20:13,572 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 01:20:13,573 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 01:20:13,574 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 197 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-13 01:20:13,581] [main] java.version = 17.0.2 [testng] 01:20:13,585 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:20:13,585 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:13,622 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-13_01-20-13.log] [testng] 01:20:13,623 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-10-13 01:20:13,625] [main] testng.directory = /data [testng] [2024-10-13 01:20:13,625] [main] testng.configDirectory = /config [testng] [2024-10-13 01:20:13,633] [main] testng.multiplier = 1.0 [testng] [2024-10-13 01:20:13,633] [main] testng.in-memory = false [testng] [2024-10-13 01:20:13,633] [main] testng.allow-missing = false [testng] [2024-10-13 01:20:13,633] [main] user.language = en [testng] [2024-10-13 01:20:13,634] [main] user.country = ${user.country} [testng] [2024-10-13 01:20:13,634] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-13 01:21:03,911] [main] ---------------------------------------- [testng] [2024-10-13 01:21:03,911] [main] Total files: 5651 [testng] [2024-10-13 01:21:03,911] [main] Scan time: 50.277 s (8 ms/file) [testng] [2024-10-13 01:21:03,911] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-13 01:22:08,080] [pool-1-thread-1] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] 01:22:08,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:22:08,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:08,082 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-13_01-22-08.log] [testng] 01:22:08,082 |-INFO in ch.qos.logback.core.sift.SiftProcessor@498b021c - End of configuration. [testng] [2024-10-13 01:22:08,326] [pool-1-thread-12] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] 01:22:08,326 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:22:08,326 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:08,327 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-13_01-22-08.log] [testng] 01:22:08,327 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2308667d - End of configuration. [testng] [2024-10-13 01:22:08,511] [pool-1-thread-11] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] 01:22:08,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:22:08,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:08,511 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-13_01-22-08.log] [testng] 01:22:08,512 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14296d48 - End of configuration. [testng] [2024-10-13 01:22:08,801] [pool-1-thread-10] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] 01:22:08,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:22:08,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:08,802 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-13_01-22-08.log] [testng] 01:22:08,803 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58590857 - End of configuration. [testng] [2024-10-13 01:22:09,028] [pool-1-thread-9] Initializing /data/clay/leica_stack.lei: [testng] 01:22:09,028 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:22:09,028 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:09,029 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-13_01-22-09.log] [testng] 01:22:09,029 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18b3cac9 - End of configuration. [testng] [2024-10-13 01:22:09,270] [pool-1-thread-8] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] 01:22:09,270 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:22:09,270 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:09,271 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-13_01-22-09.log] [testng] 01:22:09,271 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73c1a27c - End of configuration. [testng] [2024-10-13 01:22:09,756] [pool-1-thread-7] Initializing /data/david/megan/megan.lei: [testng] 01:22:09,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:22:09,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:09,757 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-13_01-22-09.log] [testng] 01:22:09,758 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7363e7cf - End of configuration. [testng] [2024-10-13 01:22:10,097] [pool-1-thread-6] Initializing /data/julie/biorad/25-65.tif: [testng] 01:22:10,098 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:22:10,098 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:10,098 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-13_01-22-10.log] [testng] 01:22:10,099 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5670a432 - End of configuration. [testng] [2024-10-13 01:22:10,653] [pool-1-thread-5] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] 01:22:10,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:22:10,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:10,655 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-13_01-22-10.log] [testng] 01:22:10,655 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50344690 - End of configuration. [testng] [2024-10-13 01:22:10,792] [pool-1-thread-4] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] 01:22:10,793 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:22:10,793 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:10,793 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-13_01-22-10.log] [testng] 01:22:10,793 |-INFO in ch.qos.logback.core.sift.SiftProcessor@452a3f31 - End of configuration. [testng] [2024-10-13 01:22:10,978] [pool-1-thread-3] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] 01:22:10,978 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:22:10,978 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:10,979 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-13_01-22-10.log] [testng] 01:22:10,979 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49cc9322 - End of configuration. [testng] [2024-10-13 01:22:12,906] [pool-1-thread-2] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] 01:22:12,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:22:12,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:12,907 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-13_01-22-12.log] [testng] 01:22:12,908 |-INFO in ch.qos.logback.core.sift.SiftProcessor@713262d7 - End of configuration. [testng] [2024-10-13 01:22:20,442] [pool-1-thread-5] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-10-13 01:22:20,749] [pool-1-thread-4] Initializing /data/oliver/o459/o459.lei: [testng] [2024-10-13 01:22:27,648] [pool-1-thread-5] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2024-10-13 01:22:29,401] [pool-1-thread-6] Initializing /data/julie/c164_1.tif: [testng] [2024-10-13 01:22:39,564] [pool-1-thread-12] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-10-13 01:22:40,888] [pool-1-thread-6] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2024-10-13 01:22:42,300] [pool-1-thread-9] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-10-13 01:22:46,066] [pool-1-thread-9] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2024-10-13 01:22:48,909] [pool-1-thread-2] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2024-10-13 01:22:53,572] [pool-1-thread-9] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-10-13 01:26:13,684] [pool-1-thread-11] Initializing /data/david/intestine/intestine.lei: [testng] [2024-10-13 01:26:32,809] [pool-1-thread-6] Initializing /data/constantin/cell6/cell6.lei: [testng] [2024-10-13 01:26:42,877] [pool-1-thread-3] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2024-10-13 01:26:59,667] [pool-1-thread-12] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2024-10-13 01:28:30,100] [pool-1-thread-10] Initializing /data/samples/Leica_sample.lei: [testng] [2024-10-13 01:28:42,029] [pool-1-thread-10] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2024-10-13 01:29:34,757] [pool-1-thread-1] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-10-13 01:30:21,409] [pool-1-thread-7] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2024-10-13 01:32:07,152] [pool-1-thread-2] Initializing /data/brian/tropo/tropo.lei: [testng] [2024-10-13 01:32:16,657] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2024-10-13 01:32:19,132] [pool-1-thread-11] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2024-10-13 01:32:29,875] [pool-1-thread-2] Initializing /data/clay/leica_stack.tif: [testng] [2024-10-13 01:32:31,082] [pool-1-thread-5] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2024-10-13 01:32:37,506] [pool-1-thread-2] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] [2024-10-13 01:32:40,037] [pool-1-thread-6] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2024-10-13 01:32:49,317] [pool-1-thread-6] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2024-10-13 01:32:52,244] [pool-1-thread-2] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2024-10-13 01:32:54,327] [pool-1-thread-6] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2024-10-13 01:33:00,823] [pool-1-thread-2] Initializing /data/brian/leica-original/050118.lei: [testng] [2024-10-13 01:33:15,267] [pool-1-thread-12] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-10-13 01:33:30,536] [pool-1-thread-11] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] [2024-10-13 01:33:32,951] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] 02:42:08,282 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:42:08,282 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:42:08,283 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-13_02-42-08.log] [testng] 02:42:08,283 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2041c9a3 - 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: 82 minutes 0 seconds Finished: SUCCESS