Started by upstream project "BIOFORMATS-test-repo" build number 225
originally caused by:
Started by user devspace
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder
[BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins7463256390392823593.sh
+ '[' leica = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_35430_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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release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] 11:08:44,306 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 11:08:44,308 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service.
[testng] 11:08:44,308 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 11:08:44,309 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 11:08:44,309 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 11:08:44,309 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 11:08:44,310 |-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] 11:08:44,310 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 11:08:44,310 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 11:08:44,311 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 11:08:44,311 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 11:08:44,311 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 11:08:44,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 11:08:44,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 11:08:44,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 11:08:44,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 11:08:44,528 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 11:08:44,529 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 11:08:44,529 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 11:08:44,529 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 11:08:44,529 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration.
[testng] 11:08:44,530 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point
[testng] 11:08:44,530 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 220 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-10-17 11:08:44,538] [main] java.version = 21
[testng] 11:08:44,541 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 11:08:44,541 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:08:44,580 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-17_11-08-44.log]
[testng] 11:08:44,581 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration.
[testng] [2024-10-17 11:08:44,583] [main] testng.directory = /data
[testng] [2024-10-17 11:08:44,583] [main] testng.configDirectory = /config
[testng] [2024-10-17 11:08:44,591] [main] testng.multiplier = 1.0
[testng] [2024-10-17 11:08:44,592] [main] testng.in-memory = false
[testng] [2024-10-17 11:08:44,592] [main] testng.allow-missing = false
[testng] [2024-10-17 11:08:44,592] [main] user.language = en
[testng] [2024-10-17 11:08:44,592] [main] user.country = ${user.country}
[testng] [2024-10-17 11:08:44,592] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-10-17 11:10:28,808] [main] ----------------------------------------
[testng] [2024-10-17 11:10:28,808] [main] Total files: 5651
[testng] [2024-10-17 11:10:28,809] [main] Scan time: 104.215 s (18 ms/file)
[testng] [2024-10-17 11:10:28,809] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 44 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-10-17 11:17:56,895] [pool-1-thread-1] Initializing /data/michael/2007-01-31_zres_sp2.lei:
[testng] 11:17:56,896 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 11:17:56,896 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:17:56,897 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-17_11-17-56.log]
[testng] 11:17:56,897 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33ba906e - End of configuration.
[testng] [2024-10-17 11:18:00,751] [pool-1-thread-12] Initializing /data/clay/leica_stack.tif:
[testng] 11:18:00,752 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 11:18:00,752 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:18:00,752 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-17_11-18-00.log]
[testng] 11:18:00,753 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2361c467 - End of configuration.
[testng] [2024-10-17 11:18:03,880] [pool-1-thread-11] Initializing /data/mark/071026-561nm check/071026-561nm check.lei:
[testng] 11:18:03,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 11:18:03,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:18:03,881 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-17_11-18-03.log]
[testng] 11:18:03,881 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c03a9ed - End of configuration.
[testng] [2024-10-17 11:18:07,405] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6/Logo.jpg:
[testng] 11:18:07,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 11:18:07,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:18:07,406 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-17_11-18-07.log]
[testng] 11:18:07,406 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a2f45fd - End of configuration.
[testng] [2024-10-17 11:18:07,868] [pool-1-thread-9] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei:
[testng] 11:18:07,868 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 11:18:07,868 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:18:07,869 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-17_11-18-07.log]
[testng] 11:18:07,869 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1276c42d - End of configuration.
[testng] [2024-10-17 11:18:10,925] [pool-1-thread-8] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg:
[testng] 11:18:10,925 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 11:18:10,925 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:18:10,926 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-17_11-18-10.log]
[testng] 11:18:10,927 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b8796eb - End of configuration.
[testng] [2024-10-17 11:18:11,339] [pool-1-thread-7] Initializing /data/simon/Leica demo/fish/fish.lei:
[testng] 11:18:11,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 11:18:11,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:18:11,341 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-17_11-18-11.log]
[testng] 11:18:11,341 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32d00999 - End of configuration.
[testng] [2024-10-17 11:18:15,619] [pool-1-thread-6] Initializing /data/brian/leica-original/050118.lei:
[testng] 11:18:15,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 11:18:15,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:18:15,620 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-17_11-18-15.log]
[testng] 11:18:15,621 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23f469c2 - End of configuration.
[testng] [2024-10-17 11:18:22,488] [pool-1-thread-5] Initializing /data/constantin/cell6/Quant_Image_00.jpg:
[testng] 11:18:22,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 11:18:22,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:18:22,489 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-17_11-18-22.log]
[testng] 11:18:22,489 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3392a533 - End of configuration.
[testng] [2024-10-17 11:18:22,605] [pool-1-thread-4] Initializing /data/martin/samples-SP2/samples-SP2.lei:
[testng] 11:18:22,605 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 11:18:22,605 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:18:22,606 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-17_11-18-22.log]
[testng] 11:18:22,606 |-INFO in ch.qos.logback.core.sift.SiftProcessor@395430c - End of configuration.
[testng] [2024-10-17 11:18:24,877] [pool-1-thread-3] Initializing /data/joel/sequential scan 2/sequential scan 2.lei:
[testng] 11:18:24,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 11:18:24,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:18:24,878 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-17_11-18-24.log]
[testng] 11:18:24,878 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f4ae7 - End of configuration.
[testng] [2024-10-17 11:18:26,912] [pool-1-thread-2] Initializing /data/samples/Leica_sample.lei:
[testng] 11:18:26,912 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 11:18:26,912 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:18:26,913 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-17_11-18-26.log]
[testng] 11:18:26,913 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2096f2dd - End of configuration.
[testng] [2024-10-17 11:18:38,978] [pool-1-thread-8] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei:
[testng] [2024-10-17 11:18:42,697] [pool-1-thread-5] Initializing /data/david/megan/megan.lei:
[testng] [2024-10-17 11:18:45,564] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg:
[testng] [2024-10-17 11:18:49,375] [pool-1-thread-12] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei:
[testng] [2024-10-17 11:18:56,543] [pool-1-thread-10] Initializing /data/joel/sequential scan 3/sequential scan 3.lei:
[testng] [2024-10-17 11:19:12,962] [pool-1-thread-2] Initializing /data/julie/biorad/25-65.tif:
[testng] [2024-10-17 11:19:28,855] [pool-1-thread-9] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei:
[testng] [2024-10-17 11:19:38,970] [pool-1-thread-1] Initializing /data/david/intestine/intestine.lei:
[testng] [2024-10-17 11:19:41,238] [pool-1-thread-2] Initializing /data/brian/050627-leica/050628-leica.lei:
[testng] [2024-10-17 11:30:43,398] [pool-1-thread-12] Initializing /data/andrey/10310500/10310500.lei:
[testng] [2024-10-17 11:31:57,645] [pool-1-thread-8] Initializing /data/constantin/cell6/Quant_Image_01.jpg:
[testng] [2024-10-17 11:32:10,025] [pool-1-thread-8] Initializing /data/brian/tropo/tropo.lei:
[testng] [2024-10-17 11:33:58,434] [pool-1-thread-8] Initializing /data/christophe/Leica stacks/Nf5.lei:
[testng] [2024-10-17 11:41:48,259] [pool-1-thread-9] Initializing /data/constantin/cell6/Quant_Image_02.jpg:
[testng] [2024-10-17 11:42:00,307] [pool-1-thread-9] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif:
[testng] [2024-10-17 11:42:37,445] [pool-1-thread-9] Initializing /data/julie/biorad/8291mcd8_raw01.pic:
[testng] [2024-10-17 11:43:46,127] [pool-1-thread-9] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei:
[testng] [2024-10-17 11:45:14,845] [pool-1-thread-4] Initializing /data/clay/leica_stack.lei:
[testng] [2024-10-17 11:45:26,478] [pool-1-thread-3] Initializing /data/grant/Leica SP2 (25-11-10).lei:
[testng] [2024-10-17 11:45:45,938] [pool-1-thread-1] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei:
[testng] [2024-10-17 11:46:12,010] [pool-1-thread-4] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif:
[testng] [2024-10-17 11:46:23,149] [pool-1-thread-10] Initializing /data/simon/Leica demo/test/test.lei:
[testng] [2024-10-17 11:46:47,847] [pool-1-thread-4] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei:
[testng] [2024-10-17 11:47:38,354] [pool-1-thread-8] Initializing /data/stjude/NIHSSE02-3.lei:
[testng] [2024-10-17 11:49:00,719] [pool-1-thread-5] Initializing /data/constantin/cell6/Graphs_1_00.jpg:
[testng] [2024-10-17 11:49:13,836] [pool-1-thread-5] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei:
[testng] [2024-10-17 11:50:47,567] [pool-1-thread-11] Initializing /data/julie/c164_1.tif:
[testng] [2024-10-17 11:51:14,875] [pool-1-thread-11] Initializing /data/constantin/cell6/Logo.jpg:
[testng] [2024-10-17 11:51:27,388] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6.lei:
[testng] [2024-10-17 11:52:29,041] [pool-1-thread-8] Initializing /data/vytas/4voxels/4voxels.lei:
[testng] [2024-10-17 11:57:04,858] [pool-1-thread-6] Initializing /data/oliver/o459/o459.lei:
[testng] [2024-10-17 11:58:04,971] [pool-1-thread-1] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg:
[testng] 13:07:04,614 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 13:07:04,614 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 13:07:04,615 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-17_13-07-04.log]
[testng] 13:07:04,615 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b1a790a - End of configuration.
Build was aborted
Calling Pipeline was cancelled
Finished: ABORTED