![[Jenkins]](/jenkins/static/316c2b55/images/svgs/logo.svg){kind=logo}
Started by upstream project "BIOFORMATS-test-repo" build number 365 originally caused by: Started by upstream project "Trigger" build number 391 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/jenkins2247487816118083546.sh + '[' leica = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_58126_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] 1 warning 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] 00:20:34,361 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:20:34,362 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service. [testng] 00:20:34,362 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:20:34,363 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:20:34,363 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:20:34,363 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:20:34,364 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:20:34,364 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:20:34,364 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:20:34,364 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:20:34,365 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:20:34,365 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:20:34,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:20:34,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:20:34,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:20:34,534 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:20:34,538 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:20:34,538 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:20:34,538 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:20:34,539 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:20:34,539 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration. [testng] 00:20:34,540 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point [testng] 00:20:34,540 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 176 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-05 00:20:34,548] [main] java.version = 17.0.2 [testng] 00:20:34,551 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:20:34,551 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:34,607 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-05_00-20-34.log] [testng] 00:20:34,608 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration. [testng] [2025-03-05 00:20:34,611] [main] testng.directory = /data [testng] [2025-03-05 00:20:34,611] [main] testng.configDirectory = /config [testng] [2025-03-05 00:20:34,624] [main] testng.multiplier = 1.0 [testng] [2025-03-05 00:20:34,625] [main] testng.in-memory = false [testng] [2025-03-05 00:20:34,626] [main] testng.allow-missing = false [testng] [2025-03-05 00:20:34,626] [main] user.language = en [testng] [2025-03-05 00:20:34,626] [main] user.country = ${user.country} [testng] [2025-03-05 00:20:34,626] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-05 00:21:12,778] [main] ---------------------------------------- [testng] [2025-03-05 00:21:12,778] [main] Total files: 5651 [testng] [2025-03-05 00:21:12,778] [main] Scan time: 38.152 s (6 ms/file) [testng] [2025-03-05 00:21:12,778] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-05 00:22:02,406] [pool-1-thread-1] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] 00:22:02,407 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:22:02,407 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:02,408 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-05_00-22-02.log] [testng] 00:22:02,409 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c3cbd55 - End of configuration. [testng] [2025-03-05 00:22:03,006] [pool-1-thread-12] Initializing /data/constantin/cell6/cell6.lei: [testng] 00:22:03,006 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:22:03,006 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:03,007 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-05_00-22-03.log] [testng] 00:22:03,007 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f774665 - End of configuration. [testng] [2025-03-05 00:22:03,370] [pool-1-thread-11] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] 00:22:03,370 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:22:03,370 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:03,371 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-05_00-22-03.log] [testng] 00:22:03,371 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22a49ac3 - End of configuration. [testng] [2025-03-05 00:22:03,427] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] 00:22:03,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:22:03,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:03,428 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-05_00-22-03.log] [testng] 00:22:03,428 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d4c46b9 - End of configuration. [testng] [2025-03-05 00:22:03,473] [pool-1-thread-9] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] 00:22:03,473 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:22:03,473 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:03,474 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-05_00-22-03.log] [testng] 00:22:03,474 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6afc430b - End of configuration. [testng] [2025-03-05 00:22:03,775] [pool-1-thread-8] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] 00:22:03,776 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:22:03,776 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:03,777 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-05_00-22-03.log] [testng] 00:22:03,777 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f2dc6a1 - End of configuration. [testng] [2025-03-05 00:22:04,402] [pool-1-thread-7] Initializing /data/brian/tropo/tropo.lei: [testng] 00:22:04,402 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:22:04,402 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:04,403 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-05_00-22-04.log] [testng] 00:22:04,403 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2df6a575 - End of configuration. [testng] [2025-03-05 00:22:04,589] [pool-1-thread-6] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] 00:22:04,589 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:22:04,589 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:04,590 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-05_00-22-04.log] [testng] 00:22:04,590 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a59648e - End of configuration. [testng] [2025-03-05 00:22:05,651] [pool-1-thread-5] Initializing /data/oliver/o459/o459.lei: [testng] 00:22:05,651 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:22:05,651 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:05,652 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-05_00-22-05.log] [testng] 00:22:05,653 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a0cc75d - End of configuration. [testng] [2025-03-05 00:22:06,185] [pool-1-thread-4] Initializing /data/david/megan/megan.lei: [testng] 00:22:06,186 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:22:06,186 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:06,186 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-05_00-22-06.log] [testng] 00:22:06,187 |-INFO in ch.qos.logback.core.sift.SiftProcessor@401de035 - End of configuration. [testng] [2025-03-05 00:22:06,539] [pool-1-thread-3] Initializing /data/david/intestine/intestine.lei: [testng] 00:22:06,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:22:06,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:06,539 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-05_00-22-06.log] [testng] 00:22:06,540 |-INFO in ch.qos.logback.core.sift.SiftProcessor@543f6a71 - End of configuration. [testng] [2025-03-05 00:22:06,819] [pool-1-thread-2] Initializing /data/stjude/NIHSSE02-3.lei: [testng] 00:22:06,819 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:22:06,819 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:22:06,820 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-05_00-22-06.log] [testng] 00:22:06,820 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5dd26cda - End of configuration. [testng] [2025-03-05 00:22:09,426] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2025-03-05 00:22:09,519] [pool-1-thread-11] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2025-03-05 00:22:12,290] [pool-1-thread-10] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] [2025-03-05 00:22:24,130] [pool-1-thread-7] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] [2025-03-05 00:22:25,572] [pool-1-thread-10] Initializing /data/andrey/10310500/10310500.lei: [testng] [2025-03-05 00:22:59,250] [pool-1-thread-2] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2025-03-05 00:23:01,816] [pool-1-thread-2] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg: [testng] [2025-03-05 00:23:05,384] [pool-1-thread-2] Initializing /data/julie/biorad/25-65.tif: [testng] [2025-03-05 00:23:13,842] [pool-1-thread-2] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] [2025-03-05 00:25:02,432] [pool-1-thread-9] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2025-03-05 00:26:02,805] [pool-1-thread-2] Initializing /data/julie/c164_1.tif: [testng] [2025-03-05 00:26:11,166] [pool-1-thread-2] Initializing /data/clay/leica_stack.lei: [testng] [2025-03-05 00:26:22,799] [pool-1-thread-2] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] [2025-03-05 00:26:40,995] [pool-1-thread-2] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2025-03-05 00:26:47,803] [pool-1-thread-2] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2025-03-05 00:27:07,864] [pool-1-thread-7] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] [2025-03-05 00:27:33,981] [pool-1-thread-3] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2025-03-05 00:27:38,728] [pool-1-thread-12] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2025-03-05 00:27:41,853] [pool-1-thread-12] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2025-03-05 00:28:14,542] [pool-1-thread-4] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2025-03-05 00:28:16,826] [pool-1-thread-4] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2025-03-05 00:29:11,777] [pool-1-thread-2] Initializing /data/samples/Leica_sample.lei: [testng] [2025-03-05 00:29:18,825] [pool-1-thread-2] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] [2025-03-05 00:29:20,808] [pool-1-thread-2] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2025-03-05 00:30:25,410] [pool-1-thread-4] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] [2025-03-05 00:30:27,310] [pool-1-thread-4] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2025-03-05 00:31:04,224] [pool-1-thread-9] Initializing /data/clay/leica_stack.tif: [testng] [2025-03-05 00:31:07,839] [pool-1-thread-9] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2025-03-05 00:31:24,187] [pool-1-thread-10] Initializing /data/brian/leica-original/050118.lei: [testng] [2025-03-05 00:31:27,406] [pool-1-thread-1] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2025-03-05 00:31:34,570] [pool-1-thread-1] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2025-03-05 00:31:54,354] [pool-1-thread-7] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2332, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 34 minutes 34 seconds Finished: SUCCESS