Started by upstream project "BIOFORMATS-test-repo" build number 366
originally caused by:
Started by upstream project "Trigger" build number 392
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/jenkins10642878049760968366.sh
+ '[' leica = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_58291_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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release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] 00:22:32,515 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15
[testng] 00:22:32,516 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - No custom configurators were discovered as a service.
[testng] 00:22:32,516 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:22:32,517 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:22:32,518 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 00:22:32,518 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 00:22:32,518 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 00:22:32,518 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:22:32,519 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:22:32,519 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 00:22:32,520 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 00:22:32,520 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 00:22:32,679 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 00:22:32,679 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 00:22:32,706 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 00:22:32,706 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 00:22:32,712 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 00:22:32,712 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 00:22:32,713 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 00:22:32,713 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 00:22:32,713 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@4310d43 - End of configuration.
[testng] 00:22:32,714 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@1b11171f - Registering current configuration as safe fallback point
[testng] 00:22:32,714 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 195 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2025-03-06 00:22:32,723] [main] java.version = 21
[testng] 00:22:32,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 00:22:32,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:22:32,765 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-06_00-22-32.log]
[testng] 00:22:32,766 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69504ae9 - End of configuration.
[testng] [2025-03-06 00:22:32,768] [main] testng.directory = /data
[testng] [2025-03-06 00:22:32,768] [main] testng.configDirectory = /config
[testng] [2025-03-06 00:22:32,776] [main] testng.multiplier = 1.0
[testng] [2025-03-06 00:22:32,776] [main] testng.in-memory = false
[testng] [2025-03-06 00:22:32,777] [main] testng.allow-missing = false
[testng] [2025-03-06 00:22:32,777] [main] user.language = en
[testng] [2025-03-06 00:22:32,777] [main] user.country = ${user.country}
[testng] [2025-03-06 00:22:32,777] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2025-03-06 00:22:48,915] [main] ----------------------------------------
[testng] [2025-03-06 00:22:48,915] [main] Total files: 5651
[testng] [2025-03-06 00:22:48,916] [main] Scan time: 16.138 s (2 ms/file)
[testng] [2025-03-06 00:22:48,916] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 44 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2025-03-06 00:23:20,435] [pool-1-thread-1] Initializing /data/samples/Leica_sample.lei:
[testng] 00:23:20,436 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 00:23:20,436 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:23:20,437 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-06_00-23-20.log]
[testng] 00:23:20,437 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56c6e497 - End of configuration.
[testng] [2025-03-06 00:23:20,773] [pool-1-thread-12] Initializing /data/david/intestine/intestine.lei:
[testng] 00:23:20,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 00:23:20,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:23:20,774 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-06_00-23-20.log]
[testng] 00:23:20,775 |-INFO in ch.qos.logback.core.sift.SiftProcessor@640272ee - End of configuration.
[testng] [2025-03-06 00:23:21,065] [pool-1-thread-11] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei:
[testng] 00:23:21,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 00:23:21,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:23:21,066 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-06_00-23-21.log]
[testng] 00:23:21,066 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e9de44 - End of configuration.
[testng] [2025-03-06 00:23:21,247] [pool-1-thread-10] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei:
[testng] 00:23:21,248 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 00:23:21,248 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:23:21,249 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-06_00-23-21.log]
[testng] 00:23:21,249 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b5d0536 - End of configuration.
[testng] [2025-03-06 00:23:21,594] [pool-1-thread-9] Initializing /data/clay/leica_stack.tif:
[testng] 00:23:21,595 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 00:23:21,595 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:23:21,596 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-06_00-23-21.log]
[testng] 00:23:21,596 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1bc53377 - End of configuration.
[testng] [2025-03-06 00:23:21,874] [pool-1-thread-8] Initializing /data/martin/samples-SP2/samples-SP2.lei:
[testng] 00:23:21,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 00:23:21,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:23:21,875 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-06_00-23-21.log]
[testng] 00:23:21,876 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14cad0c5 - End of configuration.
[testng] [2025-03-06 00:23:22,288] [pool-1-thread-7] Initializing /data/stjude/NIHSSE02-3.lei:
[testng] 00:23:22,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 00:23:22,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:23:22,289 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-06_00-23-22.log]
[testng] 00:23:22,289 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d7dd0b - End of configuration.
[testng] [2025-03-06 00:23:22,646] [pool-1-thread-6] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif:
[testng] 00:23:22,646 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 00:23:22,646 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:23:22,647 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-06_00-23-22.log]
[testng] 00:23:22,647 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b7d9443 - End of configuration.
[testng] [2025-03-06 00:23:23,129] [pool-1-thread-5] Initializing /data/grant/Leica SP2 (25-11-10).lei:
[testng] 00:23:23,130 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 00:23:23,130 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:23:23,130 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-06_00-23-23.log]
[testng] 00:23:23,131 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38c18985 - End of configuration.
[testng] [2025-03-06 00:23:23,439] [pool-1-thread-4] Initializing /data/constantin/cell6/cell6/Logo.jpg:
[testng] 00:23:23,440 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 00:23:23,440 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:23:23,440 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-06_00-23-23.log]
[testng] 00:23:23,441 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2096f2dd - End of configuration.
[testng] [2025-03-06 00:23:23,488] [pool-1-thread-3] Initializing /data/julie/biorad/8291mcd8_raw01.pic:
[testng] 00:23:23,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 00:23:23,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:23:23,489 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-06_00-23-23.log]
[testng] 00:23:23,489 |-INFO in ch.qos.logback.core.sift.SiftProcessor@103495f0 - End of configuration.
[testng] [2025-03-06 00:23:23,785] [pool-1-thread-2] Initializing /data/joel/sequential scan 3/sequential scan 3.lei:
[testng] 00:23:23,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 00:23:23,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:23:23,786 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-06_00-23-23.log]
[testng] 00:23:23,786 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1de1a3c7 - End of configuration.
[testng] [2025-03-06 00:23:28,357] [pool-1-thread-4] Initializing /data/brian/leica-original/050118.lei:
[testng] [2025-03-06 00:23:32,115] [pool-1-thread-9] Initializing /data/joel/sequential scan 2/sequential scan 2.lei:
[testng] [2025-03-06 00:23:35,926] [pool-1-thread-6] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei:
[testng] [2025-03-06 00:23:37,711] [pool-1-thread-1] Initializing /data/clay/leica_stack.lei:
[testng] [2025-03-06 00:23:38,747] [pool-1-thread-3] Initializing /data/constantin/cell6/Quant_Image_01.jpg:
[testng] [2025-03-06 00:23:41,535] [pool-1-thread-11] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei:
[testng] [2025-03-06 00:23:44,670] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg:
[testng] [2025-03-06 00:23:47,726] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg:
[testng] [2025-03-06 00:23:50,272] [pool-1-thread-3] Initializing /data/julie/c164_1.tif:
[testng] [2025-03-06 00:23:57,040] [pool-1-thread-1] Initializing /data/simon/Leica demo/fish/fish.lei:
[testng] [2025-03-06 00:24:04,413] [pool-1-thread-3] Initializing /data/constantin/cell6/Quant_Image_00.jpg:
[testng] [2025-03-06 00:24:08,456] [pool-1-thread-3] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif:
[testng] [2025-03-06 00:24:18,626] [pool-1-thread-3] Initializing /data/andrey/10310500/10310500.lei:
[testng] [2025-03-06 00:24:31,625] [pool-1-thread-7] Initializing /data/christophe/Leica stacks/Nf5.lei:
[testng] [2025-03-06 00:26:38,034] [pool-1-thread-6] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg:
[testng] [2025-03-06 00:26:42,729] [pool-1-thread-6] Initializing /data/david/megan/megan.lei:
[testng] [2025-03-06 00:27:19,767] [pool-1-thread-7] Initializing /data/brian/050627-leica/050628-leica.lei:
[testng] [2025-03-06 00:30:06,716] [pool-1-thread-12] Initializing /data/constantin/cell6/Quant_Image_02.jpg:
[testng] [2025-03-06 00:30:09,967] [pool-1-thread-12] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei:
[testng] [2025-03-06 00:30:14,345] [pool-1-thread-8] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei:
[testng] [2025-03-06 00:30:21,381] [pool-1-thread-2] Initializing /data/michael/2007-01-31_zres_sp2.lei:
[testng] [2025-03-06 00:30:23,861] [pool-1-thread-9] Initializing /data/brian/tropo/tropo.lei:
[testng] [2025-03-06 00:30:35,326] [pool-1-thread-2] Initializing /data/mark/071026-561nm check/071026-561nm check.lei:
[testng] [2025-03-06 00:30:40,477] [pool-1-thread-9] Initializing /data/simon/Leica demo/test/test.lei:
[testng] [2025-03-06 00:31:59,414] [pool-1-thread-5] Initializing /data/constantin/cell6/cell6.lei:
[testng] [2025-03-06 00:32:14,388] [pool-1-thread-10] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei:
[testng] [2025-03-06 00:32:44,627] [pool-1-thread-8] Initializing /data/constantin/cell6/Logo.jpg:
[testng] [2025-03-06 00:32:47,217] [pool-1-thread-8] Initializing /data/oliver/o459/o459.lei:
[testng] [2025-03-06 00:33:00,009] [pool-1-thread-12] Initializing /data/vytas/4voxels/4voxels.lei:
[testng] [2025-03-06 00:33:10,832] [pool-1-thread-4] Initializing /data/julie/biorad/25-65.tif:
[testng] [2025-03-06 00:33:17,898] [pool-1-thread-4] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei:
[testng] [2025-03-06 00:33:35,171] [pool-1-thread-6] Initializing /data/constantin/cell6/Graphs_1_00.jpg:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 2332, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 40 minutes 33 seconds
Finished: SUCCESS