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Started by upstream project "BIOFORMATS-test-repo" build number 294 originally caused by: Started by upstream project "Trigger" build number 313 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/jenkins4317682466082195492.sh + '[' leica = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_46405_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] 00:24:43,610 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:24:43,611 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:24:43,611 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:24:43,612 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:24:43,613 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:24:43,613 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:24:43,613 |-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] 00:24:43,613 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:24:43,614 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:24:43,614 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:24:43,614 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:24:43,615 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:24:43,786 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:24:43,786 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:24:43,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:24:43,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:24:43,813 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:24:43,813 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:24:43,813 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:24:43,813 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:24:43,813 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:24:43,814 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:24:43,814 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 200 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-18 00:24:43,823] [main] java.version = 17.0.2 [testng] 00:24:43,826 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:24:43,826 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:43,865 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-18_00-24-43.log] [testng] 00:24:43,866 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-12-18 00:24:43,868] [main] testng.directory = /data [testng] [2024-12-18 00:24:43,868] [main] testng.configDirectory = /config [testng] [2024-12-18 00:24:43,877] [main] testng.multiplier = 1.0 [testng] [2024-12-18 00:24:43,878] [main] testng.in-memory = false [testng] [2024-12-18 00:24:43,878] [main] testng.allow-missing = false [testng] [2024-12-18 00:24:43,878] [main] user.language = en [testng] [2024-12-18 00:24:43,878] [main] user.country = ${user.country} [testng] [2024-12-18 00:24:43,878] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-18 00:27:45,123] [main] ---------------------------------------- [testng] [2024-12-18 00:27:45,123] [main] Total files: 5651 [testng] [2024-12-18 00:27:45,123] [main] Scan time: 181.245 s (32 ms/file) [testng] [2024-12-18 00:27:45,124] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-18 00:32:30,263] [pool-1-thread-1] Initializing /data/julie/biorad/25-65.tif: [testng] 00:32:30,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:32:30,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:30,264 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-18_00-32-30.log] [testng] 00:32:30,265 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ce23a2e - End of configuration. [testng] [2024-12-18 00:32:36,972] [pool-1-thread-12] Initializing /data/brian/leica-original/050118.lei: [testng] 00:32:36,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:32:36,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:36,973 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-18_00-32-36.log] [testng] 00:32:36,973 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c5e9642 - End of configuration. [testng] [2024-12-18 00:32:47,722] [pool-1-thread-11] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] 00:32:47,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:32:47,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:47,723 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-18_00-32-47.log] [testng] 00:32:47,723 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7dc9a95c - End of configuration. [testng] [2024-12-18 00:32:52,176] [pool-1-thread-10] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] 00:32:52,176 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:32:52,177 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:32:52,177 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-18_00-32-52.log] [testng] 00:32:52,177 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30714281 - End of configuration. [testng] [2024-12-18 00:33:04,368] [pool-1-thread-9] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] 00:33:04,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:33:04,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:04,369 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-18_00-33-04.log] [testng] 00:33:04,369 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40cc72af - End of configuration. [testng] [2024-12-18 00:33:25,626] [pool-1-thread-8] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] 00:33:25,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:33:25,627 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:25,627 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-18_00-33-25.log] [testng] 00:33:25,628 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4349a500 - End of configuration. [testng] [2024-12-18 00:33:27,070] [pool-1-thread-7] Initializing /data/david/intestine/intestine.lei: [testng] 00:33:27,070 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:33:27,070 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:27,070 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-18_00-33-27.log] [testng] 00:33:27,071 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e232df6 - End of configuration. [testng] [2024-12-18 00:33:34,047] [pool-1-thread-6] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] 00:33:34,047 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:33:34,047 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:34,048 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-18_00-33-34.log] [testng] 00:33:34,048 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2967bc1f - End of configuration. [testng] [2024-12-18 00:33:40,197] [pool-1-thread-5] Initializing /data/clay/leica_stack.lei: [testng] 00:33:40,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:33:40,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:40,198 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-18_00-33-40.log] [testng] 00:33:40,199 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ed4c075 - End of configuration. [testng] [2024-12-18 00:33:43,562] [pool-1-thread-4] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] 00:33:43,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:33:43,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:43,563 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-18_00-33-43.log] [testng] 00:33:43,564 |-INFO in ch.qos.logback.core.sift.SiftProcessor@446d9bc2 - End of configuration. [testng] [2024-12-18 00:33:46,678] [pool-1-thread-3] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] 00:33:46,678 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:33:46,678 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:46,679 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-18_00-33-46.log] [testng] 00:33:46,679 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1bc99f16 - End of configuration. [testng] [2024-12-18 00:33:50,602] [pool-1-thread-2] Initializing /data/julie/c164_1.tif: [testng] 00:33:50,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:33:50,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:33:50,603 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-18_00-33-50.log] [testng] 00:33:50,603 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d71a4c6 - End of configuration. [testng] [2024-12-18 00:34:10,419] [pool-1-thread-8] Initializing /data/brian/tropo/tropo.lei: [testng] [2024-12-18 00:34:24,293] [pool-1-thread-2] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2024-12-18 00:34:47,364] [pool-1-thread-1] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2024-12-18 00:35:34,561] [pool-1-thread-4] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-12-18 00:36:27,346] [pool-1-thread-5] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2024-12-18 00:36:44,726] [pool-1-thread-3] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2024-12-18 00:37:11,917] [pool-1-thread-8] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-12-18 00:39:19,788] [pool-1-thread-5] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2024-12-18 00:39:40,513] [pool-1-thread-5] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] [2024-12-18 00:39:45,796] [pool-1-thread-5] Initializing /data/samples/Leica_sample.lei: [testng] [2024-12-18 00:40:11,383] [pool-1-thread-5] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2024-12-18 00:40:16,177] [pool-1-thread-5] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2024-12-18 00:41:30,227] [pool-1-thread-10] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] [2024-12-18 00:41:37,534] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6.lei: [testng] [2024-12-18 00:42:10,370] [pool-1-thread-2] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2024-12-18 00:45:34,701] [pool-1-thread-6] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2024-12-18 00:49:18,026] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2024-12-18 00:49:29,638] [pool-1-thread-3] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] [2024-12-18 00:50:47,546] [pool-1-thread-3] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-12-18 00:51:01,622] [pool-1-thread-3] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] [2024-12-18 00:52:21,753] [pool-1-thread-7] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2024-12-18 00:52:55,088] [pool-1-thread-7] Initializing /data/oliver/o459/o459.lei: [testng] [2024-12-18 00:53:33,008] [pool-1-thread-11] Initializing /data/david/megan/megan.lei: [testng] [2024-12-18 00:53:54,252] [pool-1-thread-9] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2024-12-18 00:56:44,551] [pool-1-thread-1] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-12-18 00:56:53,792] [pool-1-thread-1] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2024-12-18 00:59:06,995] [pool-1-thread-10] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2024-12-18 00:59:10,065] [pool-1-thread-12] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [2024-12-18 00:59:13,443] [pool-1-thread-12] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-12-18 00:59:24,767] [pool-1-thread-4] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-12-18 01:02:14,430] [pool-1-thread-6] Initializing /data/clay/leica_stack.tif: [testng] [2024-12-18 01:02:25,975] [pool-1-thread-6] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] 09:25:50,690 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 09:25:50,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:25:50,691 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-18_09-25-50.log] [testng] 09:25:50,692 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5089a72b - 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: 541 minutes 14 seconds Finished: SUCCESS