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Started by upstream project "BIOFORMATS-test-repo" build number 275 originally caused by: Started by upstream project "Trigger" build number 296 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/jenkins8509673933239144355.sh + '[' leica = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_43286_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] 00:20:49,610 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:20:49,612 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:20:49,612 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:20:49,613 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:20:49,613 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:20:49,613 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:20:49,614 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:20:49,614 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:20:49,614 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:20:49,615 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:20:49,615 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:20:49,615 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:20:49,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:20:49,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:20:49,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:20:49,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:20:49,851 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:20:49,851 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:20:49,851 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:20:49,851 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:20:49,851 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:20:49,852 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:20:49,852 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 238 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-01 00:20:49,861] [main] java.version = 17.0.2 [testng] 00:20:49,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:20:49,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:20:49,910 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-01_00-20-49.log] [testng] 00:20:49,915 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-12-01 00:20:49,918] [main] testng.directory = /data [testng] [2024-12-01 00:20:49,918] [main] testng.configDirectory = /config [testng] [2024-12-01 00:20:49,929] [main] testng.multiplier = 1.0 [testng] [2024-12-01 00:20:49,930] [main] testng.in-memory = false [testng] [2024-12-01 00:20:49,930] [main] testng.allow-missing = false [testng] [2024-12-01 00:20:49,930] [main] user.language = en [testng] [2024-12-01 00:20:49,930] [main] user.country = ${user.country} [testng] [2024-12-01 00:20:49,930] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-01 00:21:00,790] [main] ---------------------------------------- [testng] [2024-12-01 00:21:00,791] [main] Total files: 5651 [testng] [2024-12-01 00:21:00,791] [main] Scan time: 10.86 s (1 ms/file) [testng] [2024-12-01 00:21:00,791] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 44 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-01 00:21:20,142] [pool-1-thread-1] Initializing /data/martin/samples-SP2/samples-SP2.lei: [testng] 00:21:20,142 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:21:20,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:20,145 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-01_00-21-20.log] [testng] 00:21:20,145 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32beedbf - End of configuration. [testng] [2024-12-01 00:21:20,296] [pool-1-thread-12] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei: [testng] 00:21:20,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:21:20,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:20,297 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-01_00-21-20.log] [testng] 00:21:20,297 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4df747ce - End of configuration. [testng] [2024-12-01 00:21:20,387] [pool-1-thread-11] Initializing /data/christophe/Leica stacks/Nf5.lei: [testng] 00:21:20,387 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:21:20,388 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:20,388 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-01_00-21-20.log] [testng] 00:21:20,389 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6afc430b - End of configuration. [testng] [2024-12-01 00:21:20,562] [pool-1-thread-10] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei: [testng] 00:21:20,562 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:21:20,562 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:20,563 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-01_00-21-20.log] [testng] 00:21:20,563 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3aec538c - End of configuration. [testng] [2024-12-01 00:21:20,725] [pool-1-thread-9] Initializing /data/clay/leica_stack.lei: [testng] 00:21:20,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:21:20,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:20,726 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-01_00-21-20.log] [testng] 00:21:20,727 |-INFO in ch.qos.logback.core.sift.SiftProcessor@271ca8e2 - End of configuration. [testng] [2024-12-01 00:21:20,880] [pool-1-thread-8] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei: [testng] 00:21:20,881 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:21:20,881 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:20,882 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-01_00-21-20.log] [testng] 00:21:20,882 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1623033b - End of configuration. [testng] [2024-12-01 00:21:21,264] [pool-1-thread-7] Initializing /data/david/megan/megan.lei: [testng] 00:21:21,264 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:21:21,264 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:21,265 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-01_00-21-21.log] [testng] 00:21:21,265 |-INFO in ch.qos.logback.core.sift.SiftProcessor@543f6a71 - End of configuration. [testng] [2024-12-01 00:21:21,468] [pool-1-thread-6] Initializing /data/julie/biorad/25-65.tif: [testng] 00:21:21,469 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:21:21,469 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:21,469 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-01_00-21-21.log] [testng] 00:21:21,470 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ad66698 - End of configuration. [testng] [2024-12-01 00:21:21,735] [pool-1-thread-5] Initializing /data/constantin/cell6/Quant_Image_01.jpg: [testng] 00:21:21,735 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:21:21,735 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:21,735 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-01_00-21-21.log] [testng] 00:21:21,736 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6116d0d3 - End of configuration. [testng] [2024-12-01 00:21:21,769] [pool-1-thread-4] Initializing /data/constantin/cell6/Quant_Image_00.jpg: [testng] 00:21:21,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:21:21,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:21,770 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-01_00-21-21.log] [testng] 00:21:21,770 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e1e0c34 - End of configuration. [testng] [2024-12-01 00:21:21,791] [pool-1-thread-3] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei: [testng] 00:21:21,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:21:21,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:21,792 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-01_00-21-21.log] [testng] 00:21:21,792 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9738c71 - End of configuration. [testng] [2024-12-01 00:21:22,014] [pool-1-thread-2] Initializing /data/michael/2007-01-31_zres_sp2.lei: [testng] 00:21:22,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:21:22,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:21:22,015 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-01_00-21-22.log] [testng] 00:21:22,015 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b56173a - End of configuration. [testng] [2024-12-01 00:21:24,102] [pool-1-thread-4] Initializing /data/constantin/cell6/Logo.jpg: [testng] [2024-12-01 00:21:24,178] [pool-1-thread-5] Initializing /data/oliver/o459/o459.lei: [testng] [2024-12-01 00:21:26,254] [pool-1-thread-4] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei: [testng] [2024-12-01 00:21:26,834] [pool-1-thread-6] Initializing /data/julie/c164_1.tif: [testng] [2024-12-01 00:21:30,360] [pool-1-thread-12] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei: [testng] [2024-12-01 00:21:31,205] [pool-1-thread-9] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei: [testng] [2024-12-01 00:21:34,457] [pool-1-thread-2] Initializing /data/constantin/cell6/Graphs_1_00.jpg: [testng] [2024-12-01 00:21:34,802] [pool-1-thread-6] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg: [testng] [2024-12-01 00:21:36,365] [pool-1-thread-2] Initializing /data/simon/Leica demo/test/test.lei: [testng] [2024-12-01 00:21:37,228] [pool-1-thread-6] Initializing /data/andrey/10310500/10310500.lei: [testng] [2024-12-01 00:23:18,918] [pool-1-thread-11] Initializing /data/david/intestine/intestine.lei: [testng] [2024-12-01 00:23:29,328] [pool-1-thread-9] Initializing /data/constantin/cell6/cell6.lei: [testng] [2024-12-01 00:23:37,093] [pool-1-thread-3] Initializing /data/brian/050627-leica/050628-leica.lei: [testng] [2024-12-01 00:23:56,872] [pool-1-thread-12] Initializing /data/joel/sequential scan 3/sequential scan 3.lei: [testng] [2024-12-01 00:25:18,130] [pool-1-thread-10] Initializing /data/samples/Leica_sample.lei: [testng] [2024-12-01 00:25:29,881] [pool-1-thread-10] Initializing /data/mark/071026-561nm check/071026-561nm check.lei: [testng] [2024-12-01 00:26:09,560] [pool-1-thread-1] Initializing /data/grant/Leica SP2 (25-11-10).lei: [testng] [2024-12-01 00:26:40,609] [pool-1-thread-7] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei: [testng] [2024-12-01 00:27:40,551] [pool-1-thread-2] Initializing /data/brian/tropo/tropo.lei: [testng] [2024-12-01 00:27:45,748] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg: [testng] [2024-12-01 00:27:47,179] [pool-1-thread-11] Initializing /data/stjude/NIHSSE02-3.lei: [testng] [2024-12-01 00:27:51,232] [pool-1-thread-4] Initializing /data/clay/leica_stack.tif: [testng] [2024-12-01 00:27:53,797] [pool-1-thread-2] Initializing /data/simon/Leica demo/fish/fish.lei: [testng] [2024-12-01 00:27:55,634] [pool-1-thread-4] Initializing /data/julie/biorad/8291mcd8_raw01.pic: [testng] [2024-12-01 00:27:56,044] [pool-1-thread-9] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif: [testng] [2024-12-01 00:28:01,477] [pool-1-thread-9] Initializing /data/constantin/cell6/cell6/Logo.jpg: [testng] [2024-12-01 00:28:03,268] [pool-1-thread-9] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif: [testng] [2024-12-01 00:28:04,892] [pool-1-thread-4] Initializing /data/joel/sequential scan 2/sequential scan 2.lei: [testng] [2024-12-01 00:28:09,131] [pool-1-thread-9] Initializing /data/brian/leica-original/050118.lei: [testng] [2024-12-01 00:28:18,703] [pool-1-thread-12] Initializing /data/vytas/4voxels/4voxels.lei: [testng] [2024-12-01 00:28:26,256] [pool-1-thread-11] Initializing /data/constantin/cell6/Quant_Image_02.jpg: [testng] [2024-12-01 00:28:28,428] [pool-1-thread-11] Initializing /data/constantin/cell6/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: 25 minutes 47 seconds Finished: SUCCESS