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Started by upstream project "BIOFORMATS-test-repo" build number 299 originally caused by: Started by upstream project "Trigger" build number 321 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/jenkins16570711104787716631.sh + '[' leica = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_47231_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 00:22:27,352 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:22:27,353 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 00:22:27,353 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:22:27,354 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:22:27,354 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:22:27,354 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:22:27,355 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:22:27,355 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:22:27,355 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:22:27,356 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:22:27,356 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:22:27,356 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:22:27,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:22:27,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:22:27,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:22:27,534 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:22:27,539 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:22:27,539 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:22:27,539 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:22:27,540 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:22:27,540 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 00:22:27,540 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 00:22:27,541 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 186 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-26 00:22:27,549] [main] java.version = 21 [testng] 00:22:27,552 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:22:27,552 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:27,591 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-26_00-22-27.log] [testng] 00:22:27,592 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-12-26 00:22:27,594] [main] testng.directory = /data [testng] [2024-12-26 00:22:27,594] [main] testng.configDirectory = /config [testng] [2024-12-26 00:22:27,602] [main] testng.multiplier = 1.0 [testng] [2024-12-26 00:22:27,604] [main] testng.in-memory = false [testng] [2024-12-26 00:22:27,604] [main] testng.allow-missing = false [testng] [2024-12-26 00:22:27,604] [main] user.language = en [testng] [2024-12-26 00:22:27,604] [main] user.country = ${user.country} [testng] [2024-12-26 00:22:27,604] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-26 00:22:44,637] [main] ---------------------------------------- [testng] [2024-12-26 00:22:44,637] [main] Total files: 5651 [testng] [2024-12-26 00:22:44,638] [main] Scan time: 17.033 s (3 ms/file) [testng] [2024-12-26 00:22:44,638] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-26 00:23:39,044] [pool-1-thread-1] Initializing /data/simon/Leica demo/test/test.lei: [testng] 00:23:39,045 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:23:39,045 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:39,046 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-26_00-23-39.log] [testng] 00:23:39,047 |-INFO in ch.qos.logback.core.sift.SiftProcessor@616d73c6 - End of configuration. [testng] [2024-12-26 00:23:39,708] [pool-1-thread-12] Initializing /data/julie/biorad/25-65.tif: [testng] 00:23:39,708 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:23:39,708 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:39,709 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-26_00-23-39.log] [testng] 00:23:39,709 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53ad284c - End of configuration. [testng] [2024-12-26 00:23:40,499] [pool-1-thread-11] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] 00:23:40,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:23:40,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:40,500 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-26_00-23-40.log] [testng] 00:23:40,501 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3059f35c - End of configuration. [testng] [2024-12-26 00:23:40,568] [pool-1-thread-10] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] 00:23:40,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:23:40,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:40,569 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-26_00-23-40.log] [testng] 00:23:40,570 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4795275e - End of configuration. [testng] [2024-12-26 00:23:41,185] [pool-1-thread-9] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] 00:23:41,185 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:23:41,185 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:41,186 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-26_00-23-41.log] [testng] 00:23:41,186 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6819bbab - End of configuration. [testng] [2024-12-26 00:23:41,224] [pool-1-thread-8] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] 00:23:41,224 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:23:41,224 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:41,225 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-26_00-23-41.log] [testng] 00:23:41,226 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c7120bd - End of configuration. [testng] [2024-12-26 00:23:41,912] [pool-1-thread-7] Initializing /data/andrey/10310500/10310500.lei: [testng] 00:23:41,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:23:41,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:41,913 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-26_00-23-41.log] [testng] 00:23:41,914 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50e9b308 - End of configuration. [testng] [2024-12-26 00:23:42,536] [pool-1-thread-6] Initializing /data/clay/leica_stack.tif: [testng] 00:23:42,537 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:23:42,537 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:42,537 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-26_00-23-42.log] [testng] 00:23:42,538 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6373de58 - End of configuration. [testng] [2024-12-26 00:23:43,110] [pool-1-thread-5] Initializing /data/julie/c164_1.tif: [testng] 00:23:43,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:23:43,111 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:43,111 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-26_00-23-43.log] [testng] 00:23:43,112 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39994a40 - End of configuration. [testng] [2024-12-26 00:23:44,258] [pool-1-thread-4] Initializing /data/david/intestine/intestine.lei: [testng] 00:23:44,258 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:23:44,258 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:44,259 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-26_00-23-44.log] [testng] 00:23:44,260 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2256ebe3 - End of configuration. [testng] [2024-12-26 00:23:45,039] [pool-1-thread-3] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] 00:23:45,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:23:45,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:45,040 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-26_00-23-45.log] [testng] 00:23:45,040 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d520a9f - End of configuration. [testng] [2024-12-26 00:23:45,356] [pool-1-thread-2] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] 00:23:45,356 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:23:45,356 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:45,357 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-26_00-23-45.log] [testng] 00:23:45,357 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2cd0b627 - End of configuration. [testng] [2024-12-26 00:23:52,020] [pool-1-thread-11] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2024-12-26 00:23:53,262] [pool-1-thread-9] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2024-12-26 00:23:56,362] [pool-1-thread-6] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] [2024-12-26 00:23:58,904] [pool-1-thread-12] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [2024-12-26 00:23:59,420] [pool-1-thread-10] Initializing /data/samples/Leica_sample.lei: [testng] [2024-12-26 00:24:00,852] [pool-1-thread-5] Initializing /data/david/megan/megan.lei: [testng] [2024-12-26 00:24:03,067] [pool-1-thread-6] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-12-26 00:24:05,182] [pool-1-thread-12] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] [2024-12-26 00:24:15,962] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2024-12-26 00:24:18,803] [pool-1-thread-10] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-12-26 00:24:21,994] [pool-1-thread-10] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2024-12-26 00:24:30,152] [pool-1-thread-12] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2024-12-26 00:27:00,291] [pool-1-thread-11] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-12-26 00:27:03,223] [pool-1-thread-11] Initializing /data/brian/tropo/tropo.lei: [testng] [2024-12-26 00:27:36,868] [pool-1-thread-11] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2024-12-26 00:27:38,088] [pool-1-thread-12] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] [2024-12-26 00:27:56,017] [pool-1-thread-12] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2024-12-26 00:28:02,447] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6.lei: [testng] [2024-12-26 00:28:10,109] [pool-1-thread-12] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2024-12-26 00:30:11,665] [pool-1-thread-8] Initializing /data/brian/leica-original/050118.lei: [testng] [2024-12-26 00:31:05,296] [pool-1-thread-4] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-12-26 00:32:05,937] [pool-1-thread-5] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-12-26 00:32:26,544] [pool-1-thread-9] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] [2024-12-26 00:33:01,794] [pool-1-thread-1] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] [2024-12-26 00:33:16,500] [pool-1-thread-1] Initializing /data/oliver/o459/o459.lei: [testng] [2024-12-26 00:33:28,955] [pool-1-thread-6] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2024-12-26 00:33:54,362] [pool-1-thread-4] Initializing /data/clay/leica_stack.lei: [testng] [2024-12-26 00:33:56,732] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2024-12-26 00:33:58,770] [pool-1-thread-10] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2024-12-26 00:34:07,084] [pool-1-thread-11] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] [2024-12-26 00:34:10,804] [pool-1-thread-4] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2024-12-26 00:34:19,107] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] 01:37:53,350 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:37:53,350 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:53,351 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-26_01-37-53.log] [testng] 01:37:53,352 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d763b06 - 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: 75 minutes 31 seconds Finished: SUCCESS