Started by upstream project "BIOFORMATS-test-repo" build number 68
originally caused by:
Started by upstream project "Trigger" build number 76
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/jenkins2491278971801535528.sh
+ '[' leica = slidebook ']'
++ date +%u
+ '[' 7 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_10140_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] 01:20:22,331 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:20:22,332 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service.
[testng] 01:20:22,332 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:20:22,333 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:20:22,334 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:20:22,334 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:20:22,334 |-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] 01:20:22,334 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:20:22,335 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:20:22,335 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:20:22,336 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:20:22,336 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:20:22,532 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:20:22,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:20:22,556 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:20:22,556 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:20:22,561 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:20:22,561 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:20:22,561 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:20:22,562 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:20:22,562 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration.
[testng] 01:20:22,563 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point
[testng] 01:20:22,563 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 228 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-05-19 01:20:22,572] [main] java.version = 17.0.2
[testng] 01:20:22,575 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:20:22,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:20:22,616 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-19_01-20-22.log]
[testng] 01:20:22,618 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration.
[testng] [2024-05-19 01:20:22,620] [main] testng.directory = /data
[testng] [2024-05-19 01:20:22,620] [main] testng.configDirectory = /config
[testng] [2024-05-19 01:20:22,629] [main] testng.multiplier = 1.0
[testng] [2024-05-19 01:20:22,630] [main] testng.in-memory = false
[testng] [2024-05-19 01:20:22,630] [main] testng.allow-missing = false
[testng] [2024-05-19 01:20:22,630] [main] user.language = en
[testng] [2024-05-19 01:20:22,630] [main] user.country = ${user.country}
[testng] [2024-05-19 01:20:22,630] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-05-19 01:20:33,254] [main] ----------------------------------------
[testng] [2024-05-19 01:20:33,254] [main] Total files: 5651
[testng] [2024-05-19 01:20:33,255] [main] Scan time: 10.624 s (1 ms/file)
[testng] [2024-05-19 01:20:33,255] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 44 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-05-19 01:20:51,140] [pool-1-thread-1] Initializing /data/vytas/4voxels/4voxels.lei:
[testng] 01:20:51,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:20:51,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:20:51,142 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-19_01-20-51.log]
[testng] 01:20:51,142 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b592b09 - End of configuration.
[testng] [2024-05-19 01:20:51,232] [pool-1-thread-12] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg:
[testng] 01:20:51,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:20:51,233 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:20:51,234 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-19_01-20-51.log]
[testng] 01:20:51,234 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78e69a79 - End of configuration.
[testng] [2024-05-19 01:20:51,242] [pool-1-thread-11] Initializing /data/brian/050627-leica/050628-leica.lei:
[testng] 01:20:51,242 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:20:51,242 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:20:51,243 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-19_01-20-51.log]
[testng] 01:20:51,244 |-INFO in ch.qos.logback.core.sift.SiftProcessor@414e7249 - End of configuration.
[testng] [2024-05-19 01:20:51,725] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg:
[testng] 01:20:51,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:20:51,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:20:51,727 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-19_01-20-51.log]
[testng] 01:20:51,727 |-INFO in ch.qos.logback.core.sift.SiftProcessor@486445c4 - End of configuration.
[testng] [2024-05-19 01:20:51,748] [pool-1-thread-9] Initializing /data/constantin/cell6/cell6.lei:
[testng] 01:20:51,749 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:20:51,749 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:20:51,750 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-19_01-20-51.log]
[testng] 01:20:51,750 |-INFO in ch.qos.logback.core.sift.SiftProcessor@636ee3b2 - End of configuration.
[testng] [2024-05-19 01:20:51,820] [pool-1-thread-8] Initializing /data/stjude/NIHSSE02-3.lei:
[testng] 01:20:51,821 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:20:51,821 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:20:51,822 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-19_01-20-51.log]
[testng] 01:20:51,822 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7583668c - End of configuration.
[testng] [2024-05-19 01:20:51,873] [pool-1-thread-7] Initializing /data/michael/2007-01-31_zres_sp2.lei:
[testng] 01:20:51,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:20:51,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:20:51,874 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-19_01-20-51.log]
[testng] 01:20:51,874 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7eee1880 - End of configuration.
[testng] [2024-05-19 01:20:51,917] [pool-1-thread-6] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif:
[testng] 01:20:51,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:20:51,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:20:51,919 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-19_01-20-51.log]
[testng] 01:20:51,920 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7cfd8f1a - End of configuration.
[testng] [2024-05-19 01:20:52,020] [pool-1-thread-5] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei:
[testng] 01:20:52,020 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:20:52,020 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:20:52,021 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-19_01-20-52.log]
[testng] 01:20:52,021 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68b8a2d - End of configuration.
[testng] [2024-05-19 01:20:52,072] [pool-1-thread-4] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei:
[testng] 01:20:52,073 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:20:52,073 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:20:52,074 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-19_01-20-52.log]
[testng] 01:20:52,075 |-INFO in ch.qos.logback.core.sift.SiftProcessor@214d6121 - End of configuration.
[testng] [2024-05-19 01:20:52,706] [pool-1-thread-3] Initializing /data/joel/sequential scan 3/sequential scan 3.lei:
[testng] 01:20:52,707 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:20:52,707 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:20:52,708 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-19_01-20-52.log]
[testng] 01:20:52,708 |-INFO in ch.qos.logback.core.sift.SiftProcessor@604f28b - End of configuration.
[testng] [2024-05-19 01:20:52,799] [pool-1-thread-2] Initializing /data/joel/sequential scan 2/sequential scan 2.lei:
[testng] 01:20:52,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:20:52,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:20:52,801 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-19_01-20-52.log]
[testng] 01:20:52,801 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53f3e328 - End of configuration.
[testng] [2024-05-19 01:20:54,345] [pool-1-thread-12] Initializing /data/grant/Leica SP2 (25-11-10).lei:
[testng] [2024-05-19 01:20:54,488] [pool-1-thread-10] Initializing /data/constantin/cell6/Graphs_1_00.jpg:
[testng] [2024-05-19 01:20:55,551] [pool-1-thread-6] Initializing /data/simon/Leica demo/fish/fish.lei:
[testng] [2024-05-19 01:20:55,964] [pool-1-thread-7] Initializing /data/constantin/cell6/Quant_Image_02.jpg:
[testng] [2024-05-19 01:20:55,976] [pool-1-thread-10] Initializing /data/brian/leica-original/050118.lei:
[testng] [2024-05-19 01:20:56,616] [pool-1-thread-7] Initializing /data/david/megan/megan.lei:
[testng] [2024-05-19 01:20:59,778] [pool-1-thread-8] Initializing /data/mark/071026-561nm check/071026-561nm check.lei:
[testng] [2024-05-19 01:21:06,069] [pool-1-thread-5] Initializing /data/clay/leica_stack.tif:
[testng] [2024-05-19 01:21:06,386] [pool-1-thread-5] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei:
[testng] [2024-05-19 01:21:12,924] [pool-1-thread-9] Initializing /data/martin/samples-SP2/samples-SP2.lei:
[testng] [2024-05-19 01:21:13,633] [pool-1-thread-4] Initializing /data/constantin/cell6/Logo.jpg:
[testng] [2024-05-19 01:21:13,792] [pool-1-thread-4] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei:
[testng] [2024-05-19 01:21:14,472] [pool-1-thread-3] Initializing /data/clay/leica_stack.lei:
[testng] [2024-05-19 01:21:14,594] [pool-1-thread-2] Initializing /data/simon/Leica demo/test/test.lei:
[testng] [2024-05-19 01:21:15,321] [pool-1-thread-3] Initializing /data/oliver/o459/o459.lei:
[testng] [2024-05-19 01:21:21,263] [pool-1-thread-8] Initializing /data/constantin/cell6/Quant_Image_01.jpg:
[testng] [2024-05-19 01:21:21,500] [pool-1-thread-8] Initializing /data/julie/c164_1.tif:
[testng] [2024-05-19 01:21:24,329] [pool-1-thread-7] Initializing /data/david/intestine/intestine.lei:
[testng] [2024-05-19 01:21:24,528] [pool-1-thread-5] Initializing /data/andrey/10310500/10310500.lei:
[testng] [2024-05-19 01:21:31,790] [pool-1-thread-8] Initializing /data/christophe/Leica stacks/Nf5.lei:
[testng] [2024-05-19 01:21:33,295] [pool-1-thread-12] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei:
[testng] [2024-05-19 01:21:36,059] [pool-1-thread-9] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg:
[testng] [2024-05-19 01:21:36,254] [pool-1-thread-9] Initializing /data/julie/biorad/8291mcd8_raw01.pic:
[testng] [2024-05-19 01:21:37,137] [pool-1-thread-9] Initializing /data/constantin/cell6/cell6/Logo.jpg:
[testng] [2024-05-19 01:21:37,271] [pool-1-thread-9] Initializing /data/samples/Leica_sample.lei:
[testng] [2024-05-19 01:21:37,616] [pool-1-thread-4] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei:
[testng] [2024-05-19 01:21:37,855] [pool-1-thread-9] Initializing /data/constantin/cell6/Quant_Image_00.jpg:
[testng] [2024-05-19 01:21:37,995] [pool-1-thread-9] Initializing /data/brian/tropo/tropo.lei:
[testng] [2024-05-19 01:21:39,037] [pool-1-thread-9] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif:
[testng] [2024-05-19 01:21:39,692] [pool-1-thread-9] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei:
[testng] [2024-05-19 01:21:40,161] [pool-1-thread-9] Initializing /data/julie/biorad/25-65.tif:
[testng] [2024-05-19 01:21:40,796] [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: 4 minutes 2 seconds
Finished: SUCCESS