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Started by upstream project "BIOFORMATS-test-repo" build number 66 originally caused by: Started by upstream project "Trigger" build number 74 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/jenkins1729705209745514125.sh + '[' leica = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_9812_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 test-automated: [testng] File leak detector installed [testng] 07:52:46,867 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 07:52:46,869 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 07:52:46,869 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 07:52:46,870 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 07:52:46,870 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 07:52:46,870 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 07:52:46,870 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 07:52:46,870 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 07:52:46,871 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 07:52:46,871 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 07:52:46,871 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 07:52:46,871 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 07:52:47,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 07:52:47,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 07:52:47,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 07:52:47,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 07:52:47,171 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 07:52:47,172 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 07:52:47,172 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 07:52:47,172 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 07:52:47,172 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 07:52:47,173 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 07:52:47,173 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 302 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-17 07:52:47,183] [main] java.version = 1.8.0_342 [testng] 07:52:47,186 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 07:52:47,186 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:52:47,229 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-17_07-52-47.log] [testng] 07:52:47,231 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-05-17 07:52:47,232] [main] testng.directory = /data [testng] [2024-05-17 07:52:47,233] [main] testng.configDirectory = /config [testng] [2024-05-17 07:52:47,244] [main] testng.multiplier = 1.0 [testng] [2024-05-17 07:52:47,244] [main] testng.in-memory = false [testng] [2024-05-17 07:52:47,244] [main] testng.allow-missing = false [testng] [2024-05-17 07:52:47,244] [main] user.language = en [testng] [2024-05-17 07:52:47,245] [main] user.country = ${user.country} [testng] [2024-05-17 07:52:47,245] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-05-17 07:52:55,750] [main] ---------------------------------------- [testng] [2024-05-17 07:52:55,750] [main] Total files: 5651 [testng] [2024-05-17 07:52:55,751] [main] Scan time: 8.505 s (1 ms/file) [testng] [2024-05-17 07:52:55,751] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-17 07:53:11,868] [pool-1-thread-1] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] 07:53:11,868 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 07:53:11,868 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:53:11,869 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-17_07-53-11.log] [testng] 07:53:11,870 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48120c94 - End of configuration. [testng] [2024-05-17 07:53:11,989] [pool-1-thread-12] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] 07:53:11,989 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 07:53:11,989 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:53:11,990 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-17_07-53-11.log] [testng] 07:53:11,991 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36ce150a - End of configuration. [testng] [2024-05-17 07:53:11,999] [pool-1-thread-11] Initializing /data/simon/Leica demo/test/test.lei: [testng] 07:53:12,000 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 07:53:12,000 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:53:12,000 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-17_07-53-12.log] [testng] 07:53:12,001 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f512ae4 - End of configuration. [testng] [2024-05-17 07:53:12,074] [pool-1-thread-10] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] 07:53:12,074 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 07:53:12,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:53:12,075 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-17_07-53-12.log] [testng] 07:53:12,076 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f886b - End of configuration. [testng] [2024-05-17 07:53:12,122] [pool-1-thread-9] Initializing /data/samples/Leica_sample.lei: [testng] 07:53:12,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 07:53:12,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:53:12,123 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-17_07-53-12.log] [testng] 07:53:12,123 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a23b6f3 - End of configuration. [testng] [2024-05-17 07:53:12,140] [pool-1-thread-8] Initializing /data/clay/leica_stack.lei: [testng] 07:53:12,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 07:53:12,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:53:12,141 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-17_07-53-12.log] [testng] 07:53:12,141 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58dc1f94 - End of configuration. [testng] [2024-05-17 07:53:12,163] [pool-1-thread-7] Initializing /data/brian/leica-original/050118.lei: [testng] 07:53:12,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 07:53:12,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:53:12,164 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-17_07-53-12.log] [testng] 07:53:12,164 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ff4480d - End of configuration. [testng] [2024-05-17 07:53:12,462] [pool-1-thread-6] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] 07:53:12,462 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 07:53:12,462 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:53:12,463 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-17_07-53-12.log] [testng] 07:53:12,463 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22ca8094 - End of configuration. [testng] [2024-05-17 07:53:12,497] [pool-1-thread-5] Initializing /data/julie/c164_1.tif: [testng] 07:53:12,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 07:53:12,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:53:12,498 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-17_07-53-12.log] [testng] 07:53:12,499 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35ed1447 - End of configuration. [testng] [2024-05-17 07:53:12,933] [pool-1-thread-4] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] 07:53:12,933 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 07:53:12,933 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:53:12,934 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-17_07-53-12.log] [testng] 07:53:12,934 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ab59af3 - End of configuration. [testng] [2024-05-17 07:53:12,940] [pool-1-thread-3] Initializing /data/david/megan/megan.lei: [testng] 07:53:12,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 07:53:12,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:53:12,940 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-17_07-53-12.log] [testng] 07:53:12,940 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b1f3ddf - End of configuration. [testng] [2024-05-17 07:53:12,976] [pool-1-thread-2] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] 07:53:12,976 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 07:53:12,976 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:53:12,977 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-17_07-53-12.log] [testng] 07:53:12,977 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1acf289a - End of configuration. [testng] [2024-05-17 07:53:14,087] [pool-1-thread-12] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] [2024-05-17 07:53:14,116] [pool-1-thread-4] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-05-17 07:53:14,130] [pool-1-thread-9] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2024-05-17 07:53:14,280] [pool-1-thread-2] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] [2024-05-17 07:53:14,321] [pool-1-thread-8] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] [2024-05-17 07:53:14,378] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6.lei: [testng] [2024-05-17 07:53:14,503] [pool-1-thread-8] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] [2024-05-17 07:53:14,645] [pool-1-thread-4] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2024-05-17 07:53:14,921] [pool-1-thread-12] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2024-05-17 07:53:15,357] [pool-1-thread-2] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2024-05-17 07:53:17,520] [pool-1-thread-5] Initializing /data/clay/leica_stack.tif: [testng] [2024-05-17 07:53:17,878] [pool-1-thread-5] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2024-05-17 07:53:19,257] [pool-1-thread-9] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-05-17 07:53:27,339] [pool-1-thread-4] Initializing /data/brian/tropo/tropo.lei: [testng] [2024-05-17 07:53:29,103] [pool-1-thread-4] Initializing /data/julie/biorad/25-65.tif: [testng] [2024-05-17 07:53:29,454] [pool-1-thread-6] Initializing /data/david/intestine/intestine.lei: [testng] [2024-05-17 07:53:29,775] [pool-1-thread-4] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2024-05-17 07:53:29,893] [pool-1-thread-4] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-05-17 07:53:29,989] [pool-1-thread-4] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-05-17 07:53:31,257] [pool-1-thread-8] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2024-05-17 07:53:32,749] [pool-1-thread-1] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2024-05-17 07:53:32,929] [pool-1-thread-10] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2024-05-17 07:53:33,846] [pool-1-thread-5] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-05-17 07:53:34,664] [pool-1-thread-12] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-05-17 07:53:35,899] [pool-1-thread-3] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2024-05-17 07:53:38,954] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [2024-05-17 07:53:39,091] [pool-1-thread-11] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] [2024-05-17 07:53:48,495] [pool-1-thread-3] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2024-05-17 07:53:50,443] [pool-1-thread-9] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] [2024-05-17 07:53:50,590] [pool-1-thread-9] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2024-05-17 07:53:50,725] [pool-1-thread-9] Initializing /data/oliver/o459/o459.lei: [testng] [2024-05-17 07:53:51,544] [pool-1-thread-1] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [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 30 seconds Finished: SUCCESS