Started by upstream project "BIOFORMATS-test-repo" build number 220 originally caused by: Started by upstream project "Trigger" build number 247 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/jenkins9787187307914291096.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_34859_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] 01:26:42,725 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:26:42,727 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 01:26:42,727 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:26:42,728 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:26:42,728 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:26:42,728 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:26:42,728 |-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] 01:26:42,728 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:26:42,729 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:26:42,729 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:26:42,729 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:26:42,729 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:26:42,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:26:42,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:26:42,992 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:26:42,993 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:26:43,002 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:26:43,002 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:26:43,002 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:26:43,003 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:26:43,003 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 01:26:43,004 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 01:26:43,004 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 275 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-14 01:26:43,014] [main] java.version = 1.8.0_342 [testng] 01:26:43,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:26:43,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:43,064 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-14_01-26-43.log] [testng] 01:26:43,065 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-10-14 01:26:43,067] [main] testng.directory = /data [testng] [2024-10-14 01:26:43,068] [main] testng.configDirectory = /config [testng] [2024-10-14 01:26:43,080] [main] testng.multiplier = 1.0 [testng] [2024-10-14 01:26:43,080] [main] testng.in-memory = false [testng] [2024-10-14 01:26:43,080] [main] testng.allow-missing = false [testng] [2024-10-14 01:26:43,080] [main] user.language = fr [testng] [2024-10-14 01:26:43,081] [main] user.country = FR [testng] [2024-10-14 01:26:43,081] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-14 01:27:17,898] [main] ---------------------------------------- [testng] [2024-10-14 01:27:17,898] [main] Total files: 5651 [testng] [2024-10-14 01:27:17,899] [main] Scan time: 34.817 s (6 ms/file) [testng] [2024-10-14 01:27:17,899] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-14 01:28:14,189] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] 01:28:14,189 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:28:14,189 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:14,190 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-14_01-28-14.log] [testng] 01:28:14,191 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3aeb9f5b - End of configuration. [testng] [2024-10-14 01:28:14,322] [pool-1-thread-12] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] 01:28:14,322 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:28:14,322 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:14,323 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-14_01-28-14.log] [testng] 01:28:14,324 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c49da5c - End of configuration. [testng] [2024-10-14 01:28:15,562] [pool-1-thread-11] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] 01:28:15,562 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:28:15,562 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:15,563 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-14_01-28-15.log] [testng] 01:28:15,564 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b92bf18 - End of configuration. [testng] [2024-10-14 01:28:16,007] [pool-1-thread-10] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] 01:28:16,007 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:28:16,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:16,008 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-14_01-28-16.log] [testng] 01:28:16,009 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63dca199 - End of configuration. [testng] [2024-10-14 01:28:16,408] [pool-1-thread-9] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] 01:28:16,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:28:16,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:16,409 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-14_01-28-16.log] [testng] 01:28:16,409 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60f9896d - End of configuration. [testng] [2024-10-14 01:28:17,113] [pool-1-thread-8] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] 01:28:17,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:28:17,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:17,115 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-14_01-28-17.log] [testng] 01:28:17,115 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71b250d2 - End of configuration. [testng] [2024-10-14 01:28:17,347] [pool-1-thread-7] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] 01:28:17,347 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:28:17,347 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:17,347 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-14_01-28-17.log] [testng] 01:28:17,348 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8a760fd - End of configuration. [testng] [2024-10-14 01:28:17,417] [pool-1-thread-6] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] 01:28:17,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:28:17,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:17,418 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-14_01-28-17.log] [testng] 01:28:17,418 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c4c2c95 - End of configuration. [testng] [2024-10-14 01:28:17,776] [pool-1-thread-5] Initializing /data/brian/tropo/tropo.lei: [testng] 01:28:17,776 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:28:17,776 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:17,777 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-14_01-28-17.log] [testng] 01:28:17,777 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7af09468 - End of configuration. [testng] [2024-10-14 01:28:18,311] [pool-1-thread-4] Initializing /data/oliver/o459/o459.lei: [testng] 01:28:18,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:28:18,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:18,311 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-14_01-28-18.log] [testng] 01:28:18,312 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24dad4d8 - End of configuration. [testng] [2024-10-14 01:28:19,075] [pool-1-thread-3] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] 01:28:19,075 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:28:19,076 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:19,076 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-14_01-28-19.log] [testng] 01:28:19,076 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a99d52a - End of configuration. [testng] [2024-10-14 01:28:19,607] [pool-1-thread-2] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] 01:28:19,607 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:28:19,607 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:19,608 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-14_01-28-19.log] [testng] 01:28:19,608 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c73d6d5 - End of configuration. [testng] [2024-10-14 01:28:23,300] [pool-1-thread-7] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-10-14 01:28:23,437] [pool-1-thread-1] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2024-10-14 01:28:26,080] [pool-1-thread-2] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2024-10-14 01:28:28,487] [pool-1-thread-2] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2024-10-14 01:28:29,276] [pool-1-thread-7] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2024-10-14 01:28:31,440] [pool-1-thread-8] Initializing /data/clay/leica_stack.lei: [testng] [2024-10-14 01:28:32,679] [pool-1-thread-7] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2024-10-14 01:28:37,631] [pool-1-thread-10] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-10-14 01:28:39,550] [pool-1-thread-6] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2024-10-14 01:28:41,440] [pool-1-thread-5] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2024-10-14 01:28:46,609] [pool-1-thread-8] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2024-10-14 01:31:28,417] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [2024-10-14 01:31:31,121] [pool-1-thread-3] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] [2024-10-14 01:32:03,212] [pool-1-thread-6] Initializing /data/julie/c164_1.tif: [testng] [2024-10-14 01:32:13,986] [pool-1-thread-6] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-10-14 01:32:43,167] [pool-1-thread-2] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] [2024-10-14 01:35:01,576] [pool-1-thread-11] Initializing /data/julie/biorad/25-65.tif: [testng] [2024-10-14 01:35:08,095] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6.lei: [testng] [2024-10-14 01:35:34,822] [pool-1-thread-2] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2024-10-14 01:35:42,976] [pool-1-thread-2] Initializing /data/clay/leica_stack.tif: [testng] [2024-10-14 01:35:47,278] [pool-1-thread-2] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-10-14 01:36:07,248] [pool-1-thread-9] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2024-10-14 01:36:27,541] [pool-1-thread-3] Initializing /data/samples/Leica_sample.lei: [testng] [2024-10-14 01:36:37,746] [pool-1-thread-3] Initializing /data/david/megan/megan.lei: [testng] [2024-10-14 01:37:12,516] [pool-1-thread-5] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-10-14 01:37:44,623] [pool-1-thread-8] Initializing /data/david/intestine/intestine.lei: [testng] [2024-10-14 01:38:39,310] [pool-1-thread-2] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2024-10-14 01:39:06,854] [pool-1-thread-10] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-10-14 01:39:09,109] [pool-1-thread-10] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2024-10-14 01:39:16,678] [pool-1-thread-10] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] [2024-10-14 01:39:28,683] [pool-1-thread-12] Initializing /data/brian/leica-original/050118.lei: [testng] [2024-10-14 01:39:42,548] [pool-1-thread-2] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2332, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 56 minutes 45 seconds Finished: SUCCESS