Started by upstream project "BIOFORMATS-test-repo" build number 291
originally caused by:
Started by upstream project "Trigger" build number 310
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/jenkins12242798990483890362.sh
+ '[' leica = slidebook ']'
++ date +%u
+ '[' 7 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_45912_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] 00:21:48,670 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 00:21:48,671 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service.
[testng] 00:21:48,671 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:21:48,672 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:21:48,672 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 00:21:48,673 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 00:21:48,673 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 00:21:48,673 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:21:48,673 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:21:48,674 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 00:21:48,674 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 00:21:48,674 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 00:21:48,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 00:21:48,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 00:21:48,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 00:21:48,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 00:21:48,899 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 00:21:48,899 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 00:21:48,899 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 00:21:48,899 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 00:21:48,900 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration.
[testng] 00:21:48,901 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point
[testng] 00:21:48,901 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 228 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-12-15 00:21:48,909] [main] java.version = 17.0.2
[testng] 00:21:48,912 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 00:21:48,912 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:21:48,950 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-15_00-21-48.log]
[testng] 00:21:48,952 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration.
[testng] [2024-12-15 00:21:48,954] [main] testng.directory = /data
[testng] [2024-12-15 00:21:48,954] [main] testng.configDirectory = /config
[testng] [2024-12-15 00:21:48,962] [main] testng.multiplier = 1.0
[testng] [2024-12-15 00:21:48,963] [main] testng.in-memory = false
[testng] [2024-12-15 00:21:48,963] [main] testng.allow-missing = false
[testng] [2024-12-15 00:21:48,963] [main] user.language = en
[testng] [2024-12-15 00:21:48,963] [main] user.country = ${user.country}
[testng] [2024-12-15 00:21:48,963] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-12-15 00:22:27,946] [main] ----------------------------------------
[testng] [2024-12-15 00:22:27,947] [main] Total files: 5651
[testng] [2024-12-15 00:22:27,947] [main] Scan time: 38.983 s (6 ms/file)
[testng] [2024-12-15 00:22:27,947] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 44 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-12-15 00:23:59,336] [pool-1-thread-1] Initializing /data/martin/samples-SP2/samples-SP2.lei:
[testng] 00:23:59,337 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 00:23:59,337 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:23:59,338 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-15_00-23-59.log]
[testng] 00:23:59,338 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27e0ba5f - End of configuration.
[testng] [2024-12-15 00:23:59,771] [pool-1-thread-12] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei:
[testng] 00:23:59,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 00:23:59,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:23:59,772 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-15_00-23-59.log]
[testng] 00:23:59,773 |-INFO in ch.qos.logback.core.sift.SiftProcessor@349c9378 - End of configuration.
[testng] [2024-12-15 00:24:00,145] [pool-1-thread-11] Initializing /data/christophe/Leica stacks/Nf5.lei:
[testng] 00:24:00,145 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 00:24:00,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:24:00,147 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-15_00-24-00.log]
[testng] 00:24:00,147 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12389cda - End of configuration.
[testng] [2024-12-15 00:24:00,676] [pool-1-thread-10] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei:
[testng] 00:24:00,676 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 00:24:00,676 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:24:00,677 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-15_00-24-00.log]
[testng] 00:24:00,677 |-INFO in ch.qos.logback.core.sift.SiftProcessor@435f1078 - End of configuration.
[testng] [2024-12-15 00:24:01,096] [pool-1-thread-9] Initializing /data/clay/leica_stack.lei:
[testng] 00:24:01,097 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 00:24:01,097 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:24:01,098 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-15_00-24-01.log]
[testng] 00:24:01,098 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22a49ac3 - End of configuration.
[testng] [2024-12-15 00:24:01,528] [pool-1-thread-8] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei:
[testng] 00:24:01,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 00:24:01,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:24:01,529 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-15_00-24-01.log]
[testng] 00:24:01,529 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1bab989a - End of configuration.
[testng] [2024-12-15 00:24:02,297] [pool-1-thread-7] Initializing /data/david/megan/megan.lei:
[testng] 00:24:02,297 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 00:24:02,297 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:24:02,298 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-15_00-24-02.log]
[testng] 00:24:02,298 |-INFO in ch.qos.logback.core.sift.SiftProcessor@632aac67 - End of configuration.
[testng] [2024-12-15 00:24:02,781] [pool-1-thread-6] Initializing /data/julie/biorad/25-65.tif:
[testng] 00:24:02,781 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 00:24:02,781 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:24:02,782 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-15_00-24-02.log]
[testng] 00:24:02,782 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68d53b81 - End of configuration.
[testng] [2024-12-15 00:24:03,642] [pool-1-thread-5] Initializing /data/constantin/cell6/Quant_Image_01.jpg:
[testng] 00:24:03,642 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 00:24:03,642 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:24:03,643 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-15_00-24-03.log]
[testng] 00:24:03,643 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ee5ebbd - End of configuration.
[testng] [2024-12-15 00:24:03,825] [pool-1-thread-4] Initializing /data/constantin/cell6/Quant_Image_00.jpg:
[testng] 00:24:03,825 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 00:24:03,825 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:24:03,826 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-15_00-24-03.log]
[testng] 00:24:03,826 |-INFO in ch.qos.logback.core.sift.SiftProcessor@509b8cbd - End of configuration.
[testng] [2024-12-15 00:24:04,002] [pool-1-thread-3] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei:
[testng] 00:24:04,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 00:24:04,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:24:04,003 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-15_00-24-04.log]
[testng] 00:24:04,003 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35123f6 - End of configuration.
[testng] [2024-12-15 00:24:05,453] [pool-1-thread-2] Initializing /data/michael/2007-01-31_zres_sp2.lei:
[testng] 00:24:05,453 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 00:24:05,453 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:24:05,454 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-15_00-24-05.log]
[testng] 00:24:05,454 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a59648e - End of configuration.
[testng] [2024-12-15 00:24:12,663] [pool-1-thread-5] Initializing /data/constantin/cell6/Logo.jpg:
[testng] [2024-12-15 00:24:12,924] [pool-1-thread-4] Initializing /data/oliver/o459/o459.lei:
[testng] [2024-12-15 00:24:20,603] [pool-1-thread-5] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei:
[testng] [2024-12-15 00:24:24,171] [pool-1-thread-6] Initializing /data/julie/c164_1.tif:
[testng] [2024-12-15 00:24:37,697] [pool-1-thread-12] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei:
[testng] [2024-12-15 00:24:40,001] [pool-1-thread-9] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei:
[testng] [2024-12-15 00:24:41,674] [pool-1-thread-6] Initializing /data/constantin/cell6/Graphs_1_00.jpg:
[testng] [2024-12-15 00:24:45,879] [pool-1-thread-2] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg:
[testng] [2024-12-15 00:24:47,846] [pool-1-thread-6] Initializing /data/simon/Leica demo/test/test.lei:
[testng] [2024-12-15 00:24:52,511] [pool-1-thread-2] Initializing /data/andrey/10310500/10310500.lei:
[testng] [2024-12-15 00:29:39,857] [pool-1-thread-11] Initializing /data/david/intestine/intestine.lei:
[testng] [2024-12-15 00:30:11,938] [pool-1-thread-9] Initializing /data/constantin/cell6/cell6.lei:
[testng] [2024-12-15 00:30:25,071] [pool-1-thread-3] Initializing /data/brian/050627-leica/050628-leica.lei:
[testng] [2024-12-15 00:30:56,824] [pool-1-thread-12] Initializing /data/joel/sequential scan 3/sequential scan 3.lei:
[testng] [2024-12-15 00:33:44,998] [pool-1-thread-10] Initializing /data/samples/Leica_sample.lei:
[testng] [2024-12-15 00:34:02,332] [pool-1-thread-10] Initializing /data/mark/071026-561nm check/071026-561nm check.lei:
[testng] [2024-12-15 00:35:35,769] [pool-1-thread-1] Initializing /data/grant/Leica SP2 (25-11-10).lei:
[testng] [2024-12-15 00:36:53,560] [pool-1-thread-7] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei:
[testng] [2024-12-15 00:40:00,603] [pool-1-thread-6] Initializing /data/brian/tropo/tropo.lei:
[testng] [2024-12-15 00:40:10,303] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg:
[testng] [2024-12-15 00:40:15,688] [pool-1-thread-11] Initializing /data/stjude/NIHSSE02-3.lei:
[testng] [2024-12-15 00:40:32,291] [pool-1-thread-5] Initializing /data/clay/leica_stack.tif:
[testng] [2024-12-15 00:40:43,227] [pool-1-thread-6] Initializing /data/simon/Leica demo/fish/fish.lei:
[testng] [2024-12-15 00:40:46,772] [pool-1-thread-5] Initializing /data/julie/biorad/8291mcd8_raw01.pic:
[testng] [2024-12-15 00:40:57,479] [pool-1-thread-9] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif:
[testng] [2024-12-15 00:41:12,051] [pool-1-thread-5] Initializing /data/constantin/cell6/cell6/Logo.jpg:
[testng] [2024-12-15 00:41:15,483] [pool-1-thread-9] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif:
[testng] [2024-12-15 00:41:21,036] [pool-1-thread-5] Initializing /data/joel/sequential scan 2/sequential scan 2.lei:
[testng] [2024-12-15 00:41:37,037] [pool-1-thread-9] Initializing /data/brian/leica-original/050118.lei:
[testng] [2024-12-15 00:42:12,585] [pool-1-thread-12] Initializing /data/vytas/4voxels/4voxels.lei:
[testng] [2024-12-15 00:42:27,895] [pool-1-thread-11] Initializing /data/constantin/cell6/Quant_Image_02.jpg:
[testng] [2024-12-15 00:42:32,950] [pool-1-thread-11] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg:
[testng] 03:12:17,290 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 03:12:17,290 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 03:12:17,290 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-15_03-12-17.log]
[testng] 03:12:17,291 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2041c9a3 - End of configuration.
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 2332, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 170 minutes 31 seconds
Finished: SUCCESS