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Started by upstream project "BIOFORMATS-test-repo" build number 62 originally caused by: Started by upstream project "Trigger" build number 69 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/jenkins17497802469332054284.sh + '[' leica = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_9156_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 -Duser.language=fr -Duser.country=FR 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] 01:20:52,998 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:20:53,000 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 01:20:53,000 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:20:53,001 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:20:53,001 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:20:53,001 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:20:53,001 |-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] 01:20:53,001 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:20:53,002 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:20:53,002 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:20:53,002 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:20:53,002 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:20:53,216 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:20:53,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:20:53,243 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:20:53,243 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:20:53,251 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:20:53,251 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:20:53,251 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:20:53,252 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:20:53,252 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 01:20:53,253 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 01:20:53,253 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 251 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-13 01:20:53,262] [main] java.version = 1.8.0_342 [testng] 01:20:53,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:20:53,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:53,309 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-13_01-20-53.log] [testng] 01:20:53,310 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-05-13 01:20:53,312] [main] testng.directory = /data [testng] [2024-05-13 01:20:53,312] [main] testng.configDirectory = /config [testng] [2024-05-13 01:20:53,324] [main] testng.multiplier = 1.0 [testng] [2024-05-13 01:20:53,324] [main] testng.in-memory = false [testng] [2024-05-13 01:20:53,324] [main] testng.allow-missing = false [testng] [2024-05-13 01:20:53,324] [main] user.language = fr [testng] [2024-05-13 01:20:53,324] [main] user.country = FR [testng] [2024-05-13 01:20:53,324] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-05-13 01:21:00,783] [main] ---------------------------------------- [testng] [2024-05-13 01:21:00,784] [main] Total files: 5651 [testng] [2024-05-13 01:21:00,784] [main] Scan time: 7.459 s (1 ms/file) [testng] [2024-05-13 01:21:00,784] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-13 01:21:14,898] [pool-1-thread-1] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] 01:21:14,898 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:21:14,899 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:14,900 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-13_01-21-14.log] [testng] 01:21:14,900 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4351542c - End of configuration. [testng] [2024-05-13 01:21:14,934] [pool-1-thread-12] Initializing /data/samples/Leica_sample.lei: [testng] 01:21:14,934 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:21:14,934 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:14,935 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-13_01-21-14.log] [testng] 01:21:14,935 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45003c46 - End of configuration. [testng] [2024-05-13 01:21:14,953] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] 01:21:14,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:21:14,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:14,954 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-13_01-21-14.log] [testng] 01:21:14,954 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64d0c26e - End of configuration. [testng] [2024-05-13 01:21:14,962] [pool-1-thread-10] Initializing /data/simon/Leica demo/test/test.lei: [testng] 01:21:14,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:21:14,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:14,963 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-13_01-21-14.log] [testng] 01:21:14,963 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21956e6 - End of configuration. [testng] [2024-05-13 01:21:15,035] [pool-1-thread-9] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] 01:21:15,035 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:21:15,035 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:15,036 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-13_01-21-15.log] [testng] 01:21:15,036 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b082c6e - End of configuration. [testng] [2024-05-13 01:21:15,101] [pool-1-thread-8] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] 01:21:15,101 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:21:15,101 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:15,102 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-13_01-21-15.log] [testng] 01:21:15,102 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f0f6f50 - End of configuration. [testng] [2024-05-13 01:21:15,135] [pool-1-thread-7] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] 01:21:15,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:21:15,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:15,135 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-13_01-21-15.log] [testng] 01:21:15,136 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9e78cc7 - End of configuration. [testng] [2024-05-13 01:21:15,142] [pool-1-thread-6] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] 01:21:15,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:21:15,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:15,143 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-13_01-21-15.log] [testng] 01:21:15,144 |-INFO in ch.qos.logback.core.sift.SiftProcessor@206e140f - End of configuration. [testng] [2024-05-13 01:21:15,150] [pool-1-thread-5] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] 01:21:15,150 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:21:15,150 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:15,151 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-13_01-21-15.log] [testng] 01:21:15,151 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c4cf992 - End of configuration. [testng] [2024-05-13 01:21:15,173] [pool-1-thread-4] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] 01:21:15,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:21:15,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:15,174 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-13_01-21-15.log] [testng] 01:21:15,174 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7386203a - End of configuration. [testng] [2024-05-13 01:21:15,205] [pool-1-thread-3] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] 01:21:15,205 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:21:15,205 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:15,206 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-13_01-21-15.log] [testng] 01:21:15,206 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e7064d8 - End of configuration. [testng] [2024-05-13 01:21:15,569] [pool-1-thread-2] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] 01:21:15,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:21:15,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:15,570 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-13_01-21-15.log] [testng] 01:21:15,570 |-INFO in ch.qos.logback.core.sift.SiftProcessor@82a8e5c - End of configuration. [testng] [2024-05-13 01:21:16,650] [pool-1-thread-11] Initializing /data/david/megan/megan.lei: [testng] [2024-05-13 01:21:16,691] [pool-1-thread-6] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2024-05-13 01:21:16,734] [pool-1-thread-7] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2024-05-13 01:21:16,801] [pool-1-thread-12] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2024-05-13 01:21:16,832] [pool-1-thread-1] Initializing /data/julie/c164_1.tif: [testng] [2024-05-13 01:21:17,480] [pool-1-thread-2] Initializing /data/constantin/cell6/cell6.lei: [testng] [2024-05-13 01:21:18,146] [pool-1-thread-6] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-05-13 01:21:18,275] [pool-1-thread-6] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-05-13 01:21:21,562] [pool-1-thread-1] Initializing /data/clay/leica_stack.tif: [testng] [2024-05-13 01:21:21,806] [pool-1-thread-12] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2024-05-13 01:21:22,179] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2024-05-13 01:21:22,338] [pool-1-thread-1] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-05-13 01:21:22,711] [pool-1-thread-1] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2024-05-13 01:21:25,915] [pool-1-thread-5] Initializing /data/brian/leica-original/050118.lei: [testng] [2024-05-13 01:21:26,436] [pool-1-thread-9] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2024-05-13 01:21:27,058] [pool-1-thread-9] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2024-05-13 01:21:35,821] [pool-1-thread-4] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2024-05-13 01:21:36,582] [pool-1-thread-2] Initializing /data/oliver/o459/o459.lei: [testng] [2024-05-13 01:21:36,844] [pool-1-thread-8] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-05-13 01:21:37,679] [pool-1-thread-12] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] [2024-05-13 01:21:37,849] [pool-1-thread-7] Initializing /data/brian/tropo/tropo.lei: [testng] [2024-05-13 01:21:39,304] [pool-1-thread-7] Initializing /data/clay/leica_stack.lei: [testng] [2024-05-13 01:21:39,987] [pool-1-thread-7] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2024-05-13 01:21:40,161] [pool-1-thread-7] Initializing /data/david/intestine/intestine.lei: [testng] [2024-05-13 01:21:41,565] [pool-1-thread-10] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] [2024-05-13 01:21:41,941] [pool-1-thread-11] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] [2024-05-13 01:21:42,903] [pool-1-thread-11] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2024-05-13 01:21:54,184] [pool-1-thread-12] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-05-13 01:21:57,530] [pool-1-thread-8] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2024-05-13 01:21:57,704] [pool-1-thread-8] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-05-13 01:21:59,067] [pool-1-thread-11] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] [2024-05-13 01:21:59,255] [pool-1-thread-11] Initializing /data/julie/biorad/25-65.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 14 seconds Finished: SUCCESS