Started by upstream project "BIOFORMATS-test-repo" build number 120
originally caused by:
Started by upstream project "Trigger" build number 137
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/jenkins3365158554907650961.sh
+ '[' leica = slidebook ']'
++ date +%u
+ '[' 7 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_18668_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] 01:19:45,703 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:19:45,704 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service.
[testng] 01:19:45,704 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:19:45,705 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:19:45,705 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:19:45,705 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:19:45,706 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:19:45,706 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:19:45,706 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:19:45,706 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:19:45,707 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:19:45,707 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:19:45,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:19:45,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:19:45,926 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:19:45,926 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:19:45,932 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:19:45,932 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:19:45,932 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:19:45,932 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:19:45,932 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration.
[testng] 01:19:45,933 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point
[testng] 01:19:45,933 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 227 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-07-14 01:19:45,942] [main] java.version = 17.0.2
[testng] 01:19:45,945 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:19:45,945 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:19:45,983 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-14_01-19-45.log]
[testng] 01:19:45,984 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration.
[testng] [2024-07-14 01:19:45,986] [main] testng.directory = /data
[testng] [2024-07-14 01:19:45,986] [main] testng.configDirectory = /config
[testng] [2024-07-14 01:19:45,994] [main] testng.multiplier = 1.0
[testng] [2024-07-14 01:19:45,995] [main] testng.in-memory = false
[testng] [2024-07-14 01:19:45,995] [main] testng.allow-missing = false
[testng] [2024-07-14 01:19:45,995] [main] user.language = en
[testng] [2024-07-14 01:19:45,995] [main] user.country = ${user.country}
[testng] [2024-07-14 01:19:45,995] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-07-14 01:19:52,849] [main] ----------------------------------------
[testng] [2024-07-14 01:19:52,849] [main] Total files: 5651
[testng] [2024-07-14 01:19:52,850] [main] Scan time: 6.854 s (1 ms/file)
[testng] [2024-07-14 01:19:52,850] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 44 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-07-14 01:20:06,302] [pool-1-thread-1] Initializing /data/vytas/4voxels/4voxels.lei:
[testng] 01:20:06,303 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:20:06,303 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:20:06,304 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-14_01-20-06.log]
[testng] 01:20:06,304 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c787b2 - End of configuration.
[testng] [2024-07-14 01:20:06,380] [pool-1-thread-12] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg:
[testng] 01:20:06,380 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:20:06,380 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:20:06,381 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-14_01-20-06.log]
[testng] 01:20:06,381 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e55646 - End of configuration.
[testng] [2024-07-14 01:20:06,392] [pool-1-thread-11] Initializing /data/brian/050627-leica/050628-leica.lei:
[testng] 01:20:06,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:20:06,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:20:06,393 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-14_01-20-06.log]
[testng] 01:20:06,394 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a7f7f68 - End of configuration.
[testng] [2024-07-14 01:20:06,771] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg:
[testng] 01:20:06,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:20:06,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:20:06,772 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-14_01-20-06.log]
[testng] 01:20:06,772 |-INFO in ch.qos.logback.core.sift.SiftProcessor@435b1d2f - End of configuration.
[testng] [2024-07-14 01:20:06,796] [pool-1-thread-9] Initializing /data/constantin/cell6/cell6.lei:
[testng] 01:20:06,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:20:06,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:20:06,797 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-14_01-20-06.log]
[testng] 01:20:06,797 |-INFO in ch.qos.logback.core.sift.SiftProcessor@94cf7f - End of configuration.
[testng] [2024-07-14 01:20:06,838] [pool-1-thread-8] Initializing /data/stjude/NIHSSE02-3.lei:
[testng] 01:20:06,838 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:20:06,838 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:20:06,839 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-14_01-20-06.log]
[testng] 01:20:06,839 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48352220 - End of configuration.
[testng] [2024-07-14 01:20:06,872] [pool-1-thread-7] Initializing /data/michael/2007-01-31_zres_sp2.lei:
[testng] 01:20:06,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:20:06,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:20:06,873 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-14_01-20-06.log]
[testng] 01:20:06,873 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d0e2f5e - End of configuration.
[testng] [2024-07-14 01:20:06,910] [pool-1-thread-6] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif:
[testng] 01:20:06,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:20:06,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:20:06,911 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-14_01-20-06.log]
[testng] 01:20:06,912 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7687d9ad - End of configuration.
[testng] [2024-07-14 01:20:06,965] [pool-1-thread-5] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei:
[testng] 01:20:06,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:20:06,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:20:06,966 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-14_01-20-06.log]
[testng] 01:20:06,966 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38860afc - End of configuration.
[testng] [2024-07-14 01:20:07,006] [pool-1-thread-4] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei:
[testng] 01:20:07,006 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:20:07,006 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:20:07,007 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-14_01-20-07.log]
[testng] 01:20:07,007 |-INFO in ch.qos.logback.core.sift.SiftProcessor@636ee3b2 - End of configuration.
[testng] [2024-07-14 01:20:07,181] [pool-1-thread-3] Initializing /data/joel/sequential scan 3/sequential scan 3.lei:
[testng] 01:20:07,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:20:07,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:20:07,182 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-14_01-20-07.log]
[testng] 01:20:07,182 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6aca7a5 - End of configuration.
[testng] [2024-07-14 01:20:07,216] [pool-1-thread-2] Initializing /data/joel/sequential scan 2/sequential scan 2.lei:
[testng] 01:20:07,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:20:07,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:20:07,217 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-14_01-20-07.log]
[testng] 01:20:07,218 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23836026 - End of configuration.
[testng] [2024-07-14 01:20:08,051] [pool-1-thread-10] Initializing /data/grant/Leica SP2 (25-11-10).lei:
[testng] [2024-07-14 01:20:08,112] [pool-1-thread-12] Initializing /data/constantin/cell6/Graphs_1_00.jpg:
[testng] [2024-07-14 01:20:08,471] [pool-1-thread-6] Initializing /data/simon/Leica demo/fish/fish.lei:
[testng] [2024-07-14 01:20:08,727] [pool-1-thread-7] Initializing /data/brian/leica-original/050118.lei:
[testng] [2024-07-14 01:20:09,179] [pool-1-thread-12] Initializing /data/constantin/cell6/Quant_Image_02.jpg:
[testng] [2024-07-14 01:20:09,323] [pool-1-thread-12] Initializing /data/david/megan/megan.lei:
[testng] [2024-07-14 01:20:11,150] [pool-1-thread-8] Initializing /data/mark/071026-561nm check/071026-561nm check.lei:
[testng] [2024-07-14 01:20:16,749] [pool-1-thread-5] Initializing /data/clay/leica_stack.tif:
[testng] [2024-07-14 01:20:17,197] [pool-1-thread-5] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei:
[testng] [2024-07-14 01:20:23,168] [pool-1-thread-9] Initializing /data/martin/samples-SP2/samples-SP2.lei:
[testng] [2024-07-14 01:20:24,366] [pool-1-thread-4] Initializing /data/constantin/cell6/Logo.jpg:
[testng] [2024-07-14 01:20:24,508] [pool-1-thread-4] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei:
[testng] [2024-07-14 01:20:24,708] [pool-1-thread-2] Initializing /data/clay/leica_stack.lei:
[testng] [2024-07-14 01:20:25,177] [pool-1-thread-3] Initializing /data/simon/Leica demo/test/test.lei:
[testng] [2024-07-14 01:20:25,560] [pool-1-thread-2] Initializing /data/oliver/o459/o459.lei:
[testng] [2024-07-14 01:20:29,783] [pool-1-thread-8] Initializing /data/constantin/cell6/Quant_Image_01.jpg:
[testng] [2024-07-14 01:20:29,923] [pool-1-thread-8] Initializing /data/julie/c164_1.tif:
[testng] [2024-07-14 01:20:30,442] [pool-1-thread-5] Initializing /data/david/intestine/intestine.lei:
[testng] [2024-07-14 01:20:30,619] [pool-1-thread-12] Initializing /data/andrey/10310500/10310500.lei:
[testng] [2024-07-14 01:20:34,109] [pool-1-thread-8] Initializing /data/christophe/Leica stacks/Nf5.lei:
[testng] [2024-07-14 01:20:35,065] [pool-1-thread-10] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei:
[testng] [2024-07-14 01:20:37,999] [pool-1-thread-9] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg:
[testng] [2024-07-14 01:20:38,177] [pool-1-thread-9] Initializing /data/julie/biorad/8291mcd8_raw01.pic:
[testng] [2024-07-14 01:20:39,262] [pool-1-thread-9] Initializing /data/constantin/cell6/cell6/Logo.jpg:
[testng] [2024-07-14 01:20:39,451] [pool-1-thread-9] Initializing /data/samples/Leica_sample.lei:
[testng] [2024-07-14 01:20:39,982] [pool-1-thread-4] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei:
[testng] [2024-07-14 01:20:40,100] [pool-1-thread-9] Initializing /data/constantin/cell6/Quant_Image_00.jpg:
[testng] [2024-07-14 01:20:40,357] [pool-1-thread-9] Initializing /data/brian/tropo/tropo.lei:
[testng] [2024-07-14 01:20:42,189] [pool-1-thread-9] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif:
[testng] [2024-07-14 01:20:43,217] [pool-1-thread-9] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei:
[testng] [2024-07-14 01:20:43,848] [pool-1-thread-9] Initializing /data/julie/biorad/25-65.tif:
[testng] [2024-07-14 01:20:44,592] [pool-1-thread-9] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei:
[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 35 seconds
Finished: SUCCESS