Started by upstream project "BIOFORMATS-test-repo" build number 276 originally caused by: Started by upstream project "Trigger" build number 297 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/jenkins7598397071301343131.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_43450_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] 00:22:43,952 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:22:43,954 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:22:43,954 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:22:43,955 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:22:43,955 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:22:43,955 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:22:43,955 |-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] 00:22:43,955 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:22:43,956 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:22:43,956 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:22:43,956 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:22:43,956 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:22:44,186 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:22:44,186 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:22:44,215 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:22:44,215 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:22:44,223 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:22:44,223 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:22:44,224 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:22:44,224 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:22:44,224 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:22:44,225 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:22:44,225 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 269 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-02 00:22:44,235] [main] java.version = 1.8.0_342 [testng] 00:22:44,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:22:44,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:44,283 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-02_00-22-44.log] [testng] 00:22:44,285 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-02 00:22:44,287] [main] testng.directory = /data [testng] [2024-12-02 00:22:44,287] [main] testng.configDirectory = /config [testng] [2024-12-02 00:22:44,299] [main] testng.multiplier = 1.0 [testng] [2024-12-02 00:22:44,299] [main] testng.in-memory = false [testng] [2024-12-02 00:22:44,299] [main] testng.allow-missing = false [testng] [2024-12-02 00:22:44,299] [main] user.language = fr [testng] [2024-12-02 00:22:44,299] [main] user.country = FR [testng] [2024-12-02 00:22:44,299] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-02 00:22:56,005] [main] ---------------------------------------- [testng] [2024-12-02 00:22:56,005] [main] Total files: 5651 [testng] [2024-12-02 00:22:56,005] [main] Scan time: 11.706 s (2 ms/file) [testng] [2024-12-02 00:22:56,006] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-02 00:23:15,370] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] 00:23:15,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:23:15,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:15,372 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-02_00-23-15.log] [testng] 00:23:15,372 |-INFO in ch.qos.logback.core.sift.SiftProcessor@303135bc - End of configuration. [testng] [2024-12-02 00:23:15,404] [pool-1-thread-12] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] 00:23:15,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:23:15,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:15,405 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-02_00-23-15.log] [testng] 00:23:15,406 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34d36289 - End of configuration. [testng] [2024-12-02 00:23:15,939] [pool-1-thread-11] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] 00:23:15,939 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:23:15,939 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:15,940 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-02_00-23-15.log] [testng] 00:23:15,940 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18ac32c - End of configuration. [testng] [2024-12-02 00:23:16,097] [pool-1-thread-10] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] 00:23:16,097 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:23:16,097 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:16,098 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-02_00-23-16.log] [testng] 00:23:16,098 |-INFO in ch.qos.logback.core.sift.SiftProcessor@375e9d4d - End of configuration. [testng] [2024-12-02 00:23:16,259] [pool-1-thread-9] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] 00:23:16,259 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:23:16,259 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:16,260 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-02_00-23-16.log] [testng] 00:23:16,260 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5961066c - End of configuration. [testng] [2024-12-02 00:23:16,515] [pool-1-thread-8] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] 00:23:16,515 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:23:16,515 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:16,515 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-02_00-23-16.log] [testng] 00:23:16,516 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53dbc391 - End of configuration. [testng] [2024-12-02 00:23:16,655] [pool-1-thread-7] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] 00:23:16,655 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:23:16,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:16,656 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-02_00-23-16.log] [testng] 00:23:16,657 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c73d6d5 - End of configuration. [testng] [2024-12-02 00:23:16,679] [pool-1-thread-6] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] 00:23:16,679 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:23:16,679 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:16,680 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-02_00-23-16.log] [testng] 00:23:16,680 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1430e9e2 - End of configuration. [testng] [2024-12-02 00:23:16,854] [pool-1-thread-5] Initializing /data/brian/tropo/tropo.lei: [testng] 00:23:16,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:23:16,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:16,855 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-02_00-23-16.log] [testng] 00:23:16,855 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3aecc1d3 - End of configuration. [testng] [2024-12-02 00:23:17,021] [pool-1-thread-4] Initializing /data/oliver/o459/o459.lei: [testng] 00:23:17,021 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:23:17,021 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:17,021 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-02_00-23-17.log] [testng] 00:23:17,022 |-INFO in ch.qos.logback.core.sift.SiftProcessor@366da3 - End of configuration. [testng] [2024-12-02 00:23:17,214] [pool-1-thread-3] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] 00:23:17,214 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:23:17,214 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:17,215 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-02_00-23-17.log] [testng] 00:23:17,215 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fca4329 - End of configuration. [testng] [2024-12-02 00:23:17,407] [pool-1-thread-2] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] 00:23:17,407 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:23:17,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:17,408 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-02_00-23-17.log] [testng] 00:23:17,409 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73bed238 - End of configuration. [testng] [2024-12-02 00:23:19,366] [pool-1-thread-7] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-12-02 00:23:19,455] [pool-1-thread-2] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2024-12-02 00:23:20,239] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2024-12-02 00:23:21,776] [pool-1-thread-1] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2024-12-02 00:23:22,362] [pool-1-thread-7] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2024-12-02 00:23:23,650] [pool-1-thread-8] Initializing /data/clay/leica_stack.lei: [testng] [2024-12-02 00:23:24,594] [pool-1-thread-7] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2024-12-02 00:23:28,314] [pool-1-thread-10] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-12-02 00:23:30,570] [pool-1-thread-6] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2024-12-02 00:23:32,726] [pool-1-thread-5] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2024-12-02 00:23:35,684] [pool-1-thread-8] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2024-12-02 00:25:10,630] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [2024-12-02 00:25:12,432] [pool-1-thread-3] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] [2024-12-02 00:25:28,464] [pool-1-thread-6] Initializing /data/julie/c164_1.tif: [testng] [2024-12-02 00:25:36,742] [pool-1-thread-6] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-12-02 00:25:53,007] [pool-1-thread-1] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] [2024-12-02 00:28:00,433] [pool-1-thread-11] Initializing /data/julie/biorad/25-65.tif: [testng] [2024-12-02 00:28:08,679] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6.lei: [testng] [2024-12-02 00:28:30,723] [pool-1-thread-1] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2024-12-02 00:28:35,659] [pool-1-thread-1] Initializing /data/clay/leica_stack.tif: [testng] [2024-12-02 00:28:39,104] [pool-1-thread-1] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-12-02 00:28:50,167] [pool-1-thread-9] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2024-12-02 00:29:03,247] [pool-1-thread-3] Initializing /data/samples/Leica_sample.lei: [testng] [2024-12-02 00:29:09,560] [pool-1-thread-3] Initializing /data/david/megan/megan.lei: [testng] [2024-12-02 00:29:31,748] [pool-1-thread-5] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-12-02 00:29:52,318] [pool-1-thread-8] Initializing /data/david/intestine/intestine.lei: [testng] [2024-12-02 00:30:30,303] [pool-1-thread-1] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2024-12-02 00:30:45,373] [pool-1-thread-10] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-12-02 00:30:48,143] [pool-1-thread-10] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2024-12-02 00:30:56,230] [pool-1-thread-10] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] [2024-12-02 00:31:08,186] [pool-1-thread-12] Initializing /data/brian/leica-original/050118.lei: [testng] [2024-12-02 00:31:12,934] [pool-1-thread-1] 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: 27 minutes 11 seconds Finished: SUCCESS