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Started by upstream project "BIOFORMATS-test-repo" build number 273 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/jenkins3291756357095377353.sh + '[' leica = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_42958_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] 06:58:46,208 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 06:58:46,210 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 06:58:46,210 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:58:46,211 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:58:46,211 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 06:58:46,211 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 06:58:46,211 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 06:58:46,211 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:58:46,212 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:58:46,212 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 06:58:46,212 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 06:58:46,212 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 06:58:46,501 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 06:58:46,501 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 06:58:46,529 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 06:58:46,529 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 06:58:46,537 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 06:58:46,537 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 06:58:46,537 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 06:58:46,538 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 06:58:46,538 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 06:58:46,539 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 06:58:46,539 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 327 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-29 06:58:46,548] [main] java.version = 1.8.0_342 [testng] 06:58:46,552 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 06:58:46,552 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:58:46,702 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-29_06-58-46.log] [testng] 06:58:46,704 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-29 06:58:46,723] [main] testng.directory = /data [testng] [2024-11-29 06:58:46,723] [main] testng.configDirectory = /config [testng] [2024-11-29 06:58:46,886] [main] testng.multiplier = 1.0 [testng] [2024-11-29 06:58:46,886] [main] testng.in-memory = false [testng] [2024-11-29 06:58:46,886] [main] testng.allow-missing = false [testng] [2024-11-29 06:58:46,886] [main] user.language = en [testng] [2024-11-29 06:58:46,887] [main] user.country = ${user.country} [testng] [2024-11-29 06:58:46,887] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-29 06:59:42,944] [main] ---------------------------------------- [testng] [2024-11-29 06:59:42,944] [main] Total files: 5651 [testng] [2024-11-29 06:59:42,945] [main] Scan time: 56.057 s (9 ms/file) [testng] [2024-11-29 06:59:42,945] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-29 07:01:04,032] [pool-1-thread-1] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] 07:01:04,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 07:01:04,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:01:04,033 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-29_07-01-04.log] [testng] 07:01:04,034 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72f238bd - End of configuration. [testng] [2024-11-29 07:01:04,941] [pool-1-thread-12] Initializing /data/samples/Leica_sample.lei: [testng] 07:01:04,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 07:01:04,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:01:04,942 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-29_07-01-04.log] [testng] 07:01:04,943 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27c364cc - End of configuration. [testng] [2024-11-29 07:01:05,842] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] 07:01:05,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 07:01:05,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:01:05,843 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-29_07-01-05.log] [testng] 07:01:05,844 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c7b1531 - End of configuration. [testng] [2024-11-29 07:01:05,995] [pool-1-thread-10] Initializing /data/simon/Leica demo/test/test.lei: [testng] 07:01:05,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 07:01:05,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:01:05,996 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-29_07-01-05.log] [testng] 07:01:05,996 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e6a5021 - End of configuration. [testng] [2024-11-29 07:01:07,108] [pool-1-thread-9] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] 07:01:07,109 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 07:01:07,109 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:01:07,110 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-29_07-01-07.log] [testng] 07:01:07,110 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5576e48a - End of configuration. [testng] [2024-11-29 07:01:07,693] [pool-1-thread-8] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] 07:01:07,693 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 07:01:07,693 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:01:07,693 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-29_07-01-07.log] [testng] 07:01:07,694 |-INFO in ch.qos.logback.core.sift.SiftProcessor@225c7073 - End of configuration. [testng] [2024-11-29 07:01:08,150] [pool-1-thread-7] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] 07:01:08,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 07:01:08,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:01:08,152 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-29_07-01-08.log] [testng] 07:01:08,152 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d43f40f - End of configuration. [testng] [2024-11-29 07:01:08,189] [pool-1-thread-6] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] 07:01:08,189 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 07:01:08,189 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:01:08,190 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-29_07-01-08.log] [testng] 07:01:08,190 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57ecc1b3 - End of configuration. [testng] [2024-11-29 07:01:08,235] [pool-1-thread-5] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] 07:01:08,235 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 07:01:08,235 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:01:08,236 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-29_07-01-08.log] [testng] 07:01:08,237 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75b06c82 - End of configuration. [testng] [2024-11-29 07:01:08,536] [pool-1-thread-4] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] 07:01:08,536 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 07:01:08,536 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:01:08,536 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-29_07-01-08.log] [testng] 07:01:08,537 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a6c1104 - End of configuration. [testng] [2024-11-29 07:01:08,858] [pool-1-thread-3] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] 07:01:08,858 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 07:01:08,858 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:01:08,859 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-29_07-01-08.log] [testng] 07:01:08,859 |-INFO in ch.qos.logback.core.sift.SiftProcessor@760a950f - End of configuration. [testng] [2024-11-29 07:01:09,806] [pool-1-thread-2] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] 07:01:09,806 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 07:01:09,806 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:01:09,807 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-29_07-01-09.log] [testng] 07:01:09,807 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21dc7252 - End of configuration. [testng] [2024-11-29 07:01:12,673] [pool-1-thread-6] Initializing /data/david/megan/megan.lei: [testng] [2024-11-29 07:01:13,629] [pool-1-thread-11] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2024-11-29 07:01:14,308] [pool-1-thread-7] Initializing /data/julie/c164_1.tif: [testng] [2024-11-29 07:01:23,374] [pool-1-thread-12] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2024-11-29 07:01:24,973] [pool-1-thread-2] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2024-11-29 07:01:27,742] [pool-1-thread-7] Initializing /data/constantin/cell6/cell6.lei: [testng] [2024-11-29 07:01:28,565] [pool-1-thread-1] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-11-29 07:01:30,975] [pool-1-thread-1] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-11-29 07:01:33,724] [pool-1-thread-2] Initializing /data/clay/leica_stack.tif: [testng] [2024-11-29 07:01:38,677] [pool-1-thread-2] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2024-11-29 07:02:26,269] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2024-11-29 07:02:28,778] [pool-1-thread-11] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-11-29 07:02:31,169] [pool-1-thread-11] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2024-11-29 07:04:04,948] [pool-1-thread-5] Initializing /data/brian/leica-original/050118.lei: [testng] [2024-11-29 07:04:27,104] [pool-1-thread-9] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2024-11-29 07:04:31,117] [pool-1-thread-2] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2024-11-29 07:04:34,756] [pool-1-thread-9] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2024-11-29 07:07:37,776] [pool-1-thread-4] Initializing /data/oliver/o459/o459.lei: [testng] [2024-11-29 07:07:42,626] [pool-1-thread-8] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-11-29 07:07:50,738] [pool-1-thread-7] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] [2024-11-29 07:08:30,440] [pool-1-thread-6] Initializing /data/brian/tropo/tropo.lei: [testng] [2024-11-29 07:08:54,157] [pool-1-thread-6] Initializing /data/clay/leica_stack.lei: [testng] [2024-11-29 07:09:05,339] [pool-1-thread-12] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2024-11-29 07:09:06,570] [pool-1-thread-6] Initializing /data/david/intestine/intestine.lei: [testng] [2024-11-29 07:09:08,206] [pool-1-thread-12] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] [2024-11-29 07:09:34,144] [pool-1-thread-10] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] [2024-11-29 07:09:51,962] [pool-1-thread-10] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2024-11-29 07:10:46,088] [pool-1-thread-8] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-11-29 07:12:07,236] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2024-11-29 07:12:10,563] [pool-1-thread-1] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-11-29 07:12:55,583] [pool-1-thread-3] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] [2024-11-29 07:12:57,869] [pool-1-thread-3] Initializing /data/julie/biorad/25-65.tif: [testng] 08:34:23,485 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 08:34:23,485 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:34:23,486 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-29_08-34-23.log] [testng] 08:34:23,486 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a0ee80 - 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: 95 minutes 54 seconds Finished: SUCCESS