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Started by upstream project "BIOFORMATS-test-repo" build number 58 originally caused by: Started by upstream project "Trigger" build number 65 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/jenkins1554971892306933296.sh + '[' leica = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_8500_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 [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings test-automated: [testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 01:21:01,213 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:21:01,214 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 01:21:01,214 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:21:01,215 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:21:01,215 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:21:01,215 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:21:01,216 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:21:01,216 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:21:01,216 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:21:01,217 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:21:01,217 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:21:01,217 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:21:01,385 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:21:01,385 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:21:01,409 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:21:01,409 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:21:01,415 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:21:01,416 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:21:01,416 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:21:01,416 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:21:01,416 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 01:21:01,417 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 01:21:01,417 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 201 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-09 01:21:01,426] [main] java.version = 21 [testng] 01:21:01,428 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:21:01,428 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:01,468 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-09_01-21-01.log] [testng] 01:21:01,469 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-05-09 01:21:01,470] [main] testng.directory = /data [testng] [2024-05-09 01:21:01,470] [main] testng.configDirectory = /config [testng] [2024-05-09 01:21:01,479] [main] testng.multiplier = 1.0 [testng] [2024-05-09 01:21:01,479] [main] testng.in-memory = false [testng] [2024-05-09 01:21:01,479] [main] testng.allow-missing = false [testng] [2024-05-09 01:21:01,479] [main] user.language = en [testng] [2024-05-09 01:21:01,479] [main] user.country = ${user.country} [testng] [2024-05-09 01:21:01,480] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-05-09 01:21:07,899] [main] ---------------------------------------- [testng] [2024-05-09 01:21:07,899] [main] Total files: 5651 [testng] [2024-05-09 01:21:07,899] [main] Scan time: 6.419 s (1 ms/file) [testng] [2024-05-09 01:21:07,900] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-09 01:21:23,724] [pool-1-thread-1] Initializing /data/samples/Leica_sample.lei: [testng] 01:21:23,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:21:23,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:23,726 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-09_01-21-23.log] [testng] 01:21:23,726 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69d8cdf3 - End of configuration. [testng] [2024-05-09 01:21:23,761] [pool-1-thread-12] Initializing /data/david/intestine/intestine.lei: [testng] 01:21:23,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:21:23,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:23,762 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-09_01-21-23.log] [testng] 01:21:23,762 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7021f5c0 - End of configuration. [testng] [2024-05-09 01:21:23,786] [pool-1-thread-11] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] 01:21:23,786 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:21:23,787 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:23,787 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-09_01-21-23.log] [testng] 01:21:23,788 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7fae6329 - End of configuration. [testng] [2024-05-09 01:21:23,802] [pool-1-thread-10] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] 01:21:23,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:21:23,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:23,803 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-09_01-21-23.log] [testng] 01:21:23,803 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26afcd49 - End of configuration. [testng] [2024-05-09 01:21:23,857] [pool-1-thread-9] Initializing /data/clay/leica_stack.tif: [testng] 01:21:23,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:21:23,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:23,858 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-09_01-21-23.log] [testng] 01:21:23,859 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5651f6be - End of configuration. [testng] [2024-05-09 01:21:23,878] [pool-1-thread-8] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] 01:21:23,878 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:21:23,878 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:23,879 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-09_01-21-23.log] [testng] 01:21:23,879 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50c899be - End of configuration. [testng] [2024-05-09 01:21:23,947] [pool-1-thread-7] Initializing /data/stjude/NIHSSE02-3.lei: [testng] 01:21:23,947 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:21:23,947 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:23,948 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-09_01-21-23.log] [testng] 01:21:23,948 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55fe1735 - End of configuration. [testng] [2024-05-09 01:21:23,982] [pool-1-thread-6] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] 01:21:23,983 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:21:23,983 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:23,983 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-09_01-21-23.log] [testng] 01:21:23,984 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d71919f - End of configuration. [testng] [2024-05-09 01:21:24,036] [pool-1-thread-5] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] 01:21:24,036 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:21:24,036 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:24,037 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-09_01-21-24.log] [testng] 01:21:24,037 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2179fb07 - End of configuration. [testng] [2024-05-09 01:21:24,078] [pool-1-thread-4] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] 01:21:24,078 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:21:24,078 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:24,079 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-09_01-21-24.log] [testng] 01:21:24,079 |-INFO in ch.qos.logback.core.sift.SiftProcessor@686683c4 - End of configuration. [testng] [2024-05-09 01:21:24,086] [pool-1-thread-3] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] 01:21:24,086 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:21:24,086 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:24,087 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-09_01-21-24.log] [testng] 01:21:24,087 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65c7f8f8 - End of configuration. [testng] [2024-05-09 01:21:24,115] [pool-1-thread-2] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] 01:21:24,115 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:21:24,115 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:24,116 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-09_01-21-24.log] [testng] 01:21:24,116 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5994a432 - End of configuration. [testng] [2024-05-09 01:21:25,111] [pool-1-thread-4] Initializing /data/brian/leica-original/050118.lei: [testng] [2024-05-09 01:21:25,397] [pool-1-thread-1] Initializing /data/clay/leica_stack.lei: [testng] [2024-05-09 01:21:25,415] [pool-1-thread-9] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] [2024-05-09 01:21:25,474] [pool-1-thread-11] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2024-05-09 01:21:25,645] [pool-1-thread-3] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] [2024-05-09 01:21:25,800] [pool-1-thread-6] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] [2024-05-09 01:21:26,070] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2024-05-09 01:21:26,185] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2024-05-09 01:21:26,266] [pool-1-thread-3] Initializing /data/julie/c164_1.tif: [testng] [2024-05-09 01:21:26,791] [pool-1-thread-1] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2024-05-09 01:21:29,343] [pool-1-thread-7] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] [2024-05-09 01:21:29,497] [pool-1-thread-7] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2024-05-09 01:21:30,371] [pool-1-thread-7] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-05-09 01:21:31,160] [pool-1-thread-3] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2024-05-09 01:21:36,998] [pool-1-thread-9] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [2024-05-09 01:21:37,135] [pool-1-thread-9] Initializing /data/david/megan/megan.lei: [testng] [2024-05-09 01:21:38,378] [pool-1-thread-8] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2024-05-09 01:21:41,610] [pool-1-thread-2] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] [2024-05-09 01:21:41,768] [pool-1-thread-3] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2024-05-09 01:21:41,812] [pool-1-thread-2] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-05-09 01:21:42,640] [pool-1-thread-11] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] [2024-05-09 01:21:43,693] [pool-1-thread-11] Initializing /data/brian/tropo/tropo.lei: [testng] [2024-05-09 01:21:45,021] [pool-1-thread-11] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2024-05-09 01:21:50,649] [pool-1-thread-5] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2024-05-09 01:21:54,250] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6.lei: [testng] [2024-05-09 01:21:56,802] [pool-1-thread-12] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2024-05-09 01:21:57,779] [pool-1-thread-9] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-05-09 01:21:57,973] [pool-1-thread-9] Initializing /data/oliver/o459/o459.lei: [testng] [2024-05-09 01:22:00,685] [pool-1-thread-10] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-05-09 01:22:02,465] [pool-1-thread-2] Initializing /data/julie/biorad/25-65.tif: [testng] [2024-05-09 01:22:03,107] [pool-1-thread-2] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] [2024-05-09 01:22:04,040] [pool-1-thread-11] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [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 4 seconds Finished: SUCCESS