Started by upstream project "BIOFORMATS-test-repo" build number 210
originally caused by:
Started by upstream project "Trigger" build number 236
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/jenkins16401008069646994097.sh
+ '[' leica = slidebook ']'
++ date +%u
+ '[' 6 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_33271_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] WARNING: An illegal reflective access operation has occurred
[testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket
[testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener
[testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
[testng] WARNING: All illegal access operations will be denied in a future release
[testng] File leak detector installed
[testng] 01:27:15,408 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:27:15,410 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service.
[testng] 01:27:15,410 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:27:15,411 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:27:15,411 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:27:15,411 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:27:15,412 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:27:15,412 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:27:15,412 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:27:15,413 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:27:15,413 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:27:15,413 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:27:15,594 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:27:15,594 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:27:15,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:27:15,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:27:15,625 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:27:15,625 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:27:15,625 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:27:15,626 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:27:15,626 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration.
[testng] 01:27:15,627 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point
[testng] 01:27:15,627 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 215 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-10-05 01:27:15,635] [main] java.version = 11.0.16
[testng] 01:27:15,638 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:27:15,638 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:15,679 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-05_01-27-15.log]
[testng] 01:27:15,681 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
[testng] [2024-10-05 01:27:15,683] [main] testng.directory = /data
[testng] [2024-10-05 01:27:15,683] [main] testng.configDirectory = /config
[testng] [2024-10-05 01:27:15,693] [main] testng.multiplier = 1.0
[testng] [2024-10-05 01:27:15,694] [main] testng.in-memory = false
[testng] [2024-10-05 01:27:15,694] [main] testng.allow-missing = false
[testng] [2024-10-05 01:27:15,694] [main] user.language = en
[testng] [2024-10-05 01:27:15,694] [main] user.country = ${user.country}
[testng] [2024-10-05 01:27:15,694] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-10-05 01:27:25,969] [main] ----------------------------------------
[testng] [2024-10-05 01:27:25,969] [main] Total files: 5651
[testng] [2024-10-05 01:27:25,969] [main] Scan time: 10.274 s (1 ms/file)
[testng] [2024-10-05 01:27:25,969] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 44 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-10-05 01:27:41,739] [pool-1-thread-1] Initializing /data/brian/leica-original/050118.lei:
[testng] 01:27:41,740 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:27:41,740 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:41,743 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-05_01-27-41.log]
[testng] 01:27:41,743 |-INFO in ch.qos.logback.core.sift.SiftProcessor@651e3307 - End of configuration.
[testng] [2024-10-05 01:27:42,163] [pool-1-thread-12] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei:
[testng] 01:27:42,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:27:42,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:42,164 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-05_01-27-42.log]
[testng] 01:27:42,164 |-INFO in ch.qos.logback.core.sift.SiftProcessor@245f530d - End of configuration.
[testng] [2024-10-05 01:27:42,280] [pool-1-thread-11] Initializing /data/oliver/o459/o459.lei:
[testng] 01:27:42,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:27:42,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:42,281 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-05_01-27-42.log]
[testng] 01:27:42,281 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c5b6f93 - End of configuration.
[testng] [2024-10-05 01:27:42,404] [pool-1-thread-10] Initializing /data/michael/2007-01-31_zres_sp2.lei:
[testng] 01:27:42,404 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:27:42,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:42,405 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-05_01-27-42.log]
[testng] 01:27:42,406 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14ad9884 - End of configuration.
[testng] [2024-10-05 01:27:42,516] [pool-1-thread-9] Initializing /data/constantin/cell6/cell6.lei:
[testng] 01:27:42,516 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:27:42,516 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:42,517 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-05_01-27-42.log]
[testng] 01:27:42,517 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ec8a01b - End of configuration.
[testng] [2024-10-05 01:27:42,600] [pool-1-thread-8] Initializing /data/constantin/cell6/Quant_Image_01.jpg:
[testng] 01:27:42,600 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:27:42,600 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:42,601 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-05_01-27-42.log]
[testng] 01:27:42,602 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38e4ca8f - End of configuration.
[testng] [2024-10-05 01:27:42,618] [pool-1-thread-7] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei:
[testng] 01:27:42,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:27:42,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:42,619 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-05_01-27-42.log]
[testng] 01:27:42,620 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4149f100 - End of configuration.
[testng] [2024-10-05 01:27:42,694] [pool-1-thread-6] Initializing /data/mark/071026-561nm check/071026-561nm check.lei:
[testng] 01:27:42,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:27:42,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:42,695 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-05_01-27-42.log]
[testng] 01:27:42,696 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3635e5ea - End of configuration.
[testng] [2024-10-05 01:27:42,867] [pool-1-thread-5] Initializing /data/clay/leica_stack.lei:
[testng] 01:27:42,867 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:27:42,867 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:42,868 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-05_01-27-42.log]
[testng] 01:27:42,868 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74ae1766 - End of configuration.
[testng] [2024-10-05 01:27:42,953] [pool-1-thread-4] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei:
[testng] 01:27:42,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:27:42,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:42,954 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-05_01-27-42.log]
[testng] 01:27:42,954 |-INFO in ch.qos.logback.core.sift.SiftProcessor@323fc383 - End of configuration.
[testng] [2024-10-05 01:27:43,076] [pool-1-thread-3] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei:
[testng] 01:27:43,076 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:27:43,076 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:43,077 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-05_01-27-43.log]
[testng] 01:27:43,077 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b150a00 - End of configuration.
[testng] [2024-10-05 01:27:43,202] [pool-1-thread-2] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg:
[testng] 01:27:43,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:27:43,202 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:27:43,203 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-05_01-27-43.log]
[testng] 01:27:43,204 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8ec5a70 - End of configuration.
[testng] [2024-10-05 01:27:44,698] [pool-1-thread-8] Initializing /data/david/megan/megan.lei:
[testng] [2024-10-05 01:27:45,046] [pool-1-thread-2] Initializing /data/brian/050627-leica/050628-leica.lei:
[testng] [2024-10-05 01:27:49,215] [pool-1-thread-5] Initializing /data/julie/biorad/8291mcd8_raw01.pic:
[testng] [2024-10-05 01:27:50,616] [pool-1-thread-10] Initializing /data/joel/sequential scan 3/sequential scan 3.lei:
[testng] [2024-10-05 01:27:53,690] [pool-1-thread-5] Initializing /data/christophe/Leica stacks/Nf5.lei:
[testng] [2024-10-05 01:29:05,075] [pool-1-thread-4] Initializing /data/samples/Leica_sample.lei:
[testng] [2024-10-05 01:29:10,556] [pool-1-thread-4] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif:
[testng] [2024-10-05 01:29:15,112] [pool-1-thread-4] Initializing /data/andrey/10310500/10310500.lei:
[testng] [2024-10-05 01:29:18,572] [pool-1-thread-12] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg:
[testng] [2024-10-05 01:29:20,324] [pool-1-thread-12] Initializing /data/julie/c164_1.tif:
[testng] [2024-10-05 01:29:24,791] [pool-1-thread-5] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei:
[testng] [2024-10-05 01:29:27,593] [pool-1-thread-12] Initializing /data/constantin/cell6/Graphs_1_00.jpg:
[testng] [2024-10-05 01:29:29,634] [pool-1-thread-12] Initializing /data/constantin/cell6/Quant_Image_02.jpg:
[testng] [2024-10-05 01:29:30,870] [pool-1-thread-12] Initializing /data/martin/samples-SP2/samples-SP2.lei:
[testng] [2024-10-05 01:29:33,219] [pool-1-thread-7] Initializing /data/david/intestine/intestine.lei:
[testng] [2024-10-05 01:29:33,660] [pool-1-thread-5] Initializing /data/simon/Leica demo/test/test.lei:
[testng] [2024-10-05 01:30:38,318] [pool-1-thread-3] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif:
[testng] [2024-10-05 01:30:43,258] [pool-1-thread-3] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei:
[testng] [2024-10-05 01:31:17,683] [pool-1-thread-9] Initializing /data/brian/tropo/tropo.lei:
[testng] [2024-10-05 01:31:31,009] [pool-1-thread-9] Initializing /data/constantin/cell6/Logo.jpg:
[testng] [2024-10-05 01:31:32,999] [pool-1-thread-9] Initializing /data/simon/Leica demo/fish/fish.lei:
[testng] [2024-10-05 01:31:37,623] [pool-1-thread-10] Initializing /data/joel/sequential scan 2/sequential scan 2.lei:
[testng] [2024-10-05 01:31:48,221] [pool-1-thread-8] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei:
[testng] [2024-10-05 01:31:55,283] [pool-1-thread-6] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei:
[testng] [2024-10-05 01:32:46,984] [pool-1-thread-12] Initializing /data/clay/leica_stack.tif:
[testng] [2024-10-05 01:32:48,891] [pool-1-thread-12] Initializing /data/julie/biorad/25-65.tif:
[testng] [2024-10-05 01:32:52,949] [pool-1-thread-12] Initializing /data/constantin/cell6/cell6/Logo.jpg:
[testng] [2024-10-05 01:32:53,776] [pool-1-thread-7] Initializing /data/vytas/4voxels/4voxels.lei:
[testng] [2024-10-05 01:32:54,828] [pool-1-thread-12] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg:
[testng] [2024-10-05 01:32:55,922] [pool-1-thread-12] Initializing /data/grant/Leica SP2 (25-11-10).lei:
[testng] [2024-10-05 01:33:07,920] [pool-1-thread-8] Initializing /data/constantin/cell6/Quant_Image_00.jpg:
[testng] [2024-10-05 01:33:08,959] [pool-1-thread-8] Initializing /data/stjude/NIHSSE02-3.lei:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 2332, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 19 minutes 31 seconds
Finished: SUCCESS