Started by upstream project "BIOFORMATS-test-repo" build number 303 originally caused by: Started by upstream project "Trigger" build number 325 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/jenkins5503360969240294621.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_47891_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] 00:22:23,468 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:22:23,470 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:22:23,470 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:22:23,471 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:22:23,471 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:22:23,472 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:22:23,472 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:22:23,472 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:22:23,472 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:22:23,473 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:22:23,473 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:22:23,473 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:22:23,698 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:22:23,698 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:22:23,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:22:23,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:22:23,735 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:22:23,735 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:22:23,735 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:22:23,736 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:22:23,736 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:22:23,737 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:22:23,737 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 265 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-30 00:22:23,747] [main] java.version = 1.8.0_342 [testng] 00:22:23,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:22:23,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:23,796 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-30_00-22-23.log] [testng] 00:22:23,797 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-30 00:22:23,799] [main] testng.directory = /data [testng] [2024-12-30 00:22:23,800] [main] testng.configDirectory = /config [testng] [2024-12-30 00:22:23,811] [main] testng.multiplier = 1.0 [testng] [2024-12-30 00:22:23,812] [main] testng.in-memory = false [testng] [2024-12-30 00:22:23,812] [main] testng.allow-missing = false [testng] [2024-12-30 00:22:23,812] [main] user.language = fr [testng] [2024-12-30 00:22:23,812] [main] user.country = FR [testng] [2024-12-30 00:22:23,812] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-30 00:22:48,816] [main] ---------------------------------------- [testng] [2024-12-30 00:22:48,817] [main] Total files: 5651 [testng] [2024-12-30 00:22:48,817] [main] Scan time: 25.004 s (4 ms/file) [testng] [2024-12-30 00:22:48,817] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-30 00:23:45,984] [pool-1-thread-1] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] 00:23:45,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:23:45,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:45,986 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-30_00-23-45.log] [testng] 00:23:45,987 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ae37055 - End of configuration. [testng] [2024-12-30 00:23:46,805] [pool-1-thread-12] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] 00:23:46,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:23:46,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:46,806 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-30_00-23-46.log] [testng] 00:23:46,806 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4172db03 - End of configuration. [testng] [2024-12-30 00:23:46,887] [pool-1-thread-11] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] 00:23:46,888 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:23:46,888 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:46,888 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-30_00-23-46.log] [testng] 00:23:46,889 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c46b8fd - End of configuration. [testng] [2024-12-30 00:23:47,788] [pool-1-thread-10] Initializing /data/oliver/o459/o459.lei: [testng] 00:23:47,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:23:47,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:47,790 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-30_00-23-47.log] [testng] 00:23:47,790 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c4c2c95 - End of configuration. [testng] [2024-12-30 00:23:48,422] [pool-1-thread-9] Initializing /data/david/intestine/intestine.lei: [testng] 00:23:48,423 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:23:48,423 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:48,423 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-30_00-23-48.log] [testng] 00:23:48,424 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42db89e9 - End of configuration. [testng] [2024-12-30 00:23:50,043] [pool-1-thread-8] Initializing /data/simon/Leica demo/test/test.lei: [testng] 00:23:50,044 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:23:50,044 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:50,044 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-30_00-23-50.log] [testng] 00:23:50,045 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24dad4d8 - End of configuration. [testng] [2024-12-30 00:23:50,731] [pool-1-thread-7] Initializing /data/clay/leica_stack.tif: [testng] 00:23:50,731 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:23:50,731 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:50,732 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-30_00-23-50.log] [testng] 00:23:50,732 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a99d52a - End of configuration. [testng] [2024-12-30 00:23:51,107] [pool-1-thread-6] Initializing /data/stjude/NIHSSE02-3.lei: [testng] 00:23:51,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:23:51,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:51,108 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-30_00-23-51.log] [testng] 00:23:51,108 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a125e7d - End of configuration. [testng] [2024-12-30 00:23:51,581] [pool-1-thread-5] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] 00:23:51,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:23:51,582 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:51,582 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-30_00-23-51.log] [testng] 00:23:51,582 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b0b769 - End of configuration. [testng] [2024-12-30 00:23:51,630] [pool-1-thread-4] Initializing /data/brian/tropo/tropo.lei: [testng] 00:23:51,630 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:23:51,630 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:51,631 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-30_00-23-51.log] [testng] 00:23:51,631 |-INFO in ch.qos.logback.core.sift.SiftProcessor@793e9fc - End of configuration. [testng] [2024-12-30 00:23:51,984] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6.lei: [testng] 00:23:51,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:23:51,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:51,985 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-30_00-23-51.log] [testng] 00:23:51,986 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5573311a - End of configuration. [testng] [2024-12-30 00:23:52,399] [pool-1-thread-2] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] 00:23:52,399 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:23:52,399 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:52,400 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-30_00-23-52.log] [testng] 00:23:52,400 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17d61b52 - End of configuration. [testng] [2024-12-30 00:23:57,262] [pool-1-thread-12] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] [2024-12-30 00:23:58,732] [pool-1-thread-5] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2024-12-30 00:24:00,964] [pool-1-thread-7] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2024-12-30 00:24:04,585] [pool-1-thread-5] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-12-30 00:24:24,815] [pool-1-thread-4] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2024-12-30 00:25:08,272] [pool-1-thread-6] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2024-12-30 00:27:00,355] [pool-1-thread-1] Initializing /data/brian/leica-original/050118.lei: [testng] [2024-12-30 00:27:50,590] [pool-1-thread-5] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2024-12-30 00:27:55,543] [pool-1-thread-5] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] [2024-12-30 00:28:15,093] [pool-1-thread-5] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2024-12-30 00:28:30,152] [pool-1-thread-5] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2024-12-30 00:30:28,630] [pool-1-thread-11] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] [2024-12-30 00:30:31,996] [pool-1-thread-11] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2024-12-30 00:31:31,036] [pool-1-thread-9] Initializing /data/julie/biorad/25-65.tif: [testng] [2024-12-30 00:31:36,809] [pool-1-thread-3] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2024-12-30 00:31:42,778] [pool-1-thread-9] Initializing /data/samples/Leica_sample.lei: [testng] [2024-12-30 00:31:45,984] [pool-1-thread-12] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2024-12-30 00:31:54,992] [pool-1-thread-7] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] [2024-12-30 00:31:59,222] [pool-1-thread-9] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] [2024-12-30 00:32:13,911] [pool-1-thread-9] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-12-30 00:32:17,686] [pool-1-thread-7] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2024-12-30 00:32:24,330] [pool-1-thread-7] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-12-30 00:32:26,585] [pool-1-thread-7] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2024-12-30 00:32:29,179] [pool-1-thread-7] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2024-12-30 00:32:45,488] [pool-1-thread-6] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-12-30 00:33:12,553] [pool-1-thread-11] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2024-12-30 00:33:36,767] [pool-1-thread-8] Initializing /data/julie/c164_1.tif: [testng] [2024-12-30 00:33:45,438] [pool-1-thread-8] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [2024-12-30 00:33:48,817] [pool-1-thread-8] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] [2024-12-30 00:33:51,049] [pool-1-thread-8] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] [2024-12-30 00:33:55,994] [pool-1-thread-2] Initializing /data/clay/leica_stack.lei: [testng] [2024-12-30 00:34:11,332] [pool-1-thread-2] Initializing /data/david/megan/megan.lei: [testng] 01:50:47,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:50:47,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:50:47,514 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-30_01-50-47.log] [testng] 01:50:47,514 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ddc8fc - 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: 88 minutes 28 seconds Finished: SUCCESS