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Started by upstream project "BIOFORMATS-test-repo" build number 90 originally caused by: Started by upstream project "Trigger" build number 101 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/jenkins8172524948157917565.sh + '[' leica = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_13748_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] 01:21:52,041 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:21:52,043 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:21:52,043 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:21:52,043 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:21:52,044 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:21:52,044 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:21:52,044 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:21:52,044 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:21:52,045 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:21:52,045 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:21:52,046 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:21:52,046 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:21:52,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:21:52,201 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:21:52,220 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:21:52,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:21:52,225 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:21:52,225 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:21:52,226 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:21:52,226 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:21:52,226 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:21:52,227 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:21:52,227 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 182 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-12 01:21:52,235] [main] java.version = 17.0.2 [testng] 01:21:52,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:21:52,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:52,275 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-12_01-21-52.log] [testng] 01:21:52,276 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-06-12 01:21:52,278] [main] testng.directory = /data [testng] [2024-06-12 01:21:52,278] [main] testng.configDirectory = /config [testng] [2024-06-12 01:21:52,286] [main] testng.multiplier = 1.0 [testng] [2024-06-12 01:21:52,287] [main] testng.in-memory = false [testng] [2024-06-12 01:21:52,287] [main] testng.allow-missing = false [testng] [2024-06-12 01:21:52,287] [main] user.language = en [testng] [2024-06-12 01:21:52,287] [main] user.country = ${user.country} [testng] [2024-06-12 01:21:52,287] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-12 01:22:03,552] [main] ---------------------------------------- [testng] [2024-06-12 01:22:03,553] [main] Total files: 5651 [testng] [2024-06-12 01:22:03,553] [main] Scan time: 11.265 s (1 ms/file) [testng] [2024-06-12 01:22:03,553] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-12 01:22:23,393] [pool-1-thread-1] Initializing /data/vytas/4voxels/4voxels.lei: [testng] 01:22:23,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:22:23,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:23,396 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-12_01-22-23.log] [testng] 01:22:23,396 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79b61ad4 - End of configuration. [testng] [2024-06-12 01:22:23,495] [pool-1-thread-12] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] 01:22:23,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:22:23,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:23,496 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-12_01-22-23.log] [testng] 01:22:23,497 |-INFO in ch.qos.logback.core.sift.SiftProcessor@304b5b6e - End of configuration. [testng] [2024-06-12 01:22:23,514] [pool-1-thread-11] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] 01:22:23,514 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:22:23,514 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:23,519 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-12_01-22-23.log] [testng] 01:22:23,520 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e1e0c34 - End of configuration. [testng] [2024-06-12 01:22:24,126] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] 01:22:24,126 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:22:24,126 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:24,127 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-12_01-22-24.log] [testng] 01:22:24,127 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c215d3d - End of configuration. [testng] [2024-06-12 01:22:24,135] [pool-1-thread-9] Initializing /data/constantin/cell6/cell6.lei: [testng] 01:22:24,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:22:24,136 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:24,137 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-12_01-22-24.log] [testng] 01:22:24,137 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61111152 - End of configuration. [testng] [2024-06-12 01:22:24,199] [pool-1-thread-8] Initializing /data/stjude/NIHSSE02-3.lei: [testng] 01:22:24,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:22:24,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:24,200 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-12_01-22-24.log] [testng] 01:22:24,201 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a902e4c - End of configuration. [testng] [2024-06-12 01:22:24,256] [pool-1-thread-7] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] 01:22:24,256 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:22:24,256 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:24,257 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-12_01-22-24.log] [testng] 01:22:24,257 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6507aa68 - End of configuration. [testng] [2024-06-12 01:22:24,316] [pool-1-thread-6] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] 01:22:24,316 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:22:24,316 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:24,318 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-12_01-22-24.log] [testng] 01:22:24,319 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6865b5d2 - End of configuration. [testng] [2024-06-12 01:22:24,387] [pool-1-thread-5] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] 01:22:24,387 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:22:24,387 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:24,388 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-12_01-22-24.log] [testng] 01:22:24,388 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e6f32e0 - End of configuration. [testng] [2024-06-12 01:22:24,430] [pool-1-thread-4] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] 01:22:24,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:22:24,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:24,431 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-12_01-22-24.log] [testng] 01:22:24,431 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d12520a - End of configuration. [testng] [2024-06-12 01:22:24,682] [pool-1-thread-3] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] 01:22:24,682 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:22:24,682 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:24,683 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-12_01-22-24.log] [testng] 01:22:24,683 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48352220 - End of configuration. [testng] [2024-06-12 01:22:24,735] [pool-1-thread-2] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] 01:22:24,735 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:22:24,735 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:24,736 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-12_01-22-24.log] [testng] 01:22:24,737 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d0e2f5e - End of configuration. [testng] [2024-06-12 01:22:25,879] [pool-1-thread-10] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-06-12 01:22:25,948] [pool-1-thread-12] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-06-12 01:22:26,230] [pool-1-thread-6] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2024-06-12 01:22:26,756] [pool-1-thread-7] Initializing /data/brian/leica-original/050118.lei: [testng] [2024-06-12 01:22:27,291] [pool-1-thread-12] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] [2024-06-12 01:22:27,473] [pool-1-thread-12] Initializing /data/david/megan/megan.lei: [testng] [2024-06-12 01:22:29,913] [pool-1-thread-8] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2024-06-12 01:22:35,749] [pool-1-thread-5] Initializing /data/clay/leica_stack.tif: [testng] [2024-06-12 01:22:36,131] [pool-1-thread-5] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2024-06-12 01:22:42,490] [pool-1-thread-9] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] [2024-06-12 01:22:43,545] [pool-1-thread-2] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-06-12 01:22:43,742] [pool-1-thread-2] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] [2024-06-12 01:22:44,171] [pool-1-thread-3] Initializing /data/clay/leica_stack.lei: [testng] [2024-06-12 01:22:44,208] [pool-1-thread-4] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2024-06-12 01:22:45,078] [pool-1-thread-3] Initializing /data/oliver/o459/o459.lei: [testng] [2024-06-12 01:22:50,140] [pool-1-thread-12] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] [2024-06-12 01:22:50,398] [pool-1-thread-12] Initializing /data/julie/c164_1.tif: [testng] [2024-06-12 01:22:51,280] [pool-1-thread-5] Initializing /data/david/intestine/intestine.lei: [testng] [2024-06-12 01:22:51,360] [pool-1-thread-8] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-06-12 01:22:54,771] [pool-1-thread-12] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2024-06-12 01:22:55,520] [pool-1-thread-10] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] [2024-06-12 01:22:59,654] [pool-1-thread-9] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2024-06-12 01:22:59,812] [pool-1-thread-9] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] [2024-06-12 01:23:00,483] [pool-1-thread-9] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2024-06-12 01:23:00,619] [pool-1-thread-9] Initializing /data/samples/Leica_sample.lei: [testng] [2024-06-12 01:23:00,673] [pool-1-thread-2] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2024-06-12 01:23:01,121] [pool-1-thread-9] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] [2024-06-12 01:23:01,277] [pool-1-thread-9] Initializing /data/brian/tropo/tropo.lei: [testng] [2024-06-12 01:23:02,492] [pool-1-thread-9] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2024-06-12 01:23:03,275] [pool-1-thread-9] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] [2024-06-12 01:23:03,815] [pool-1-thread-9] Initializing /data/julie/biorad/25-65.tif: [testng] [2024-06-12 01:23:04,449] [pool-1-thread-9] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2332, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 3 minutes 54 seconds Finished: SUCCESS