Started by upstream project "BIOFORMATS-test-repo" build number 305
originally caused by:
Started by upstream project "Trigger" build number 327
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/jenkins1987594835776617179.sh
+ '[' leica = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_48221_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] 00:33:46,807 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 00:33:46,809 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service.
[testng] 00:33:46,809 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:33:46,810 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:33:46,810 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 00:33:46,810 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 00:33:46,811 |-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] 00:33:46,811 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:33:46,811 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:33:46,812 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 00:33:46,812 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 00:33:46,812 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 00:33:46,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 00:33:46,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 00:33:46,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 00:33:46,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 00:33:47,000 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 00:33:47,000 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 00:33:47,000 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 00:33:47,001 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 00:33:47,001 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration.
[testng] 00:33:47,002 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point
[testng] 00:33:47,002 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 191 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2025-01-01 00:33:47,010] [main] java.version = 17.0.2
[testng] 00:33:47,013 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 00:33:47,013 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:33:47,050 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-01_00-33-47.log]
[testng] 00:33:47,052 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration.
[testng] [2025-01-01 00:33:47,054] [main] testng.directory = /data
[testng] [2025-01-01 00:33:47,054] [main] testng.configDirectory = /config
[testng] [2025-01-01 00:33:47,062] [main] testng.multiplier = 1.0
[testng] [2025-01-01 00:33:47,062] [main] testng.in-memory = false
[testng] [2025-01-01 00:33:47,062] [main] testng.allow-missing = false
[testng] [2025-01-01 00:33:47,062] [main] user.language = en
[testng] [2025-01-01 00:33:47,063] [main] user.country = ${user.country}
[testng] [2025-01-01 00:33:47,063] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2025-01-01 00:34:23,160] [main] ----------------------------------------
[testng] [2025-01-01 00:34:23,160] [main] Total files: 5651
[testng] [2025-01-01 00:34:23,161] [main] Scan time: 36.097 s (6 ms/file)
[testng] [2025-01-01 00:34:23,161] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 44 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2025-01-01 00:35:14,533] [pool-1-thread-1] Initializing /data/julie/biorad/25-65.tif:
[testng] 00:35:14,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 00:35:14,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:35:14,534 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-01_00-35-14.log]
[testng] 00:35:14,535 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ed28036 - End of configuration.
[testng] [2025-01-01 00:35:15,034] [pool-1-thread-12] Initializing /data/brian/leica-original/050118.lei:
[testng] 00:35:15,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 00:35:15,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:35:15,035 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-01_00-35-15.log]
[testng] 00:35:15,036 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fc4341d - End of configuration.
[testng] [2025-01-01 00:35:15,812] [pool-1-thread-11] Initializing /data/martin/samples-SP2/samples-SP2.lei:
[testng] 00:35:15,812 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 00:35:15,812 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:35:15,812 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-01_00-35-15.log]
[testng] 00:35:15,813 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4fc66ca0 - End of configuration.
[testng] [2025-01-01 00:35:16,085] [pool-1-thread-10] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/070123_HippoQ2Q3.lei:
[testng] 00:35:16,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 00:35:16,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:35:16,086 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-01_00-35-16.log]
[testng] 00:35:16,086 |-INFO in ch.qos.logback.core.sift.SiftProcessor@418a55c4 - End of configuration.
[testng] [2025-01-01 00:35:16,298] [pool-1-thread-9] Initializing /data/joel/sequential scan 3/sequential scan 3.lei:
[testng] 00:35:16,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 00:35:16,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:35:16,300 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-01_00-35-16.log]
[testng] 00:35:16,300 |-INFO in ch.qos.logback.core.sift.SiftProcessor@145023a7 - End of configuration.
[testng] [2025-01-01 00:35:16,567] [pool-1-thread-8] Initializing /data/constantin/cell6/cell6/Quant_Image_00.jpg:
[testng] 00:35:16,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 00:35:16,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:35:16,568 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-01_00-35-16.log]
[testng] 00:35:16,568 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66ad5b88 - End of configuration.
[testng] [2025-01-01 00:35:16,601] [pool-1-thread-7] Initializing /data/david/intestine/intestine.lei:
[testng] 00:35:16,601 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 00:35:16,601 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:35:16,602 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-01_00-35-16.log]
[testng] 00:35:16,602 |-INFO in ch.qos.logback.core.sift.SiftProcessor@221233e8 - End of configuration.
[testng] [2025-01-01 00:35:16,803] [pool-1-thread-6] Initializing /data/simon/Leica demo/RNA FISH/RNA FISH.lei:
[testng] 00:35:16,803 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 00:35:16,803 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:35:16,804 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-01_00-35-16.log]
[testng] 00:35:16,804 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63aa105d - End of configuration.
[testng] [2025-01-01 00:35:17,065] [pool-1-thread-5] Initializing /data/clay/leica_stack.lei:
[testng] 00:35:17,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 00:35:17,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:35:17,066 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-01_00-35-17.log]
[testng] 00:35:17,066 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6591f8fa - End of configuration.
[testng] [2025-01-01 00:35:17,477] [pool-1-thread-4] Initializing /data/clay/leica_stack-exported/leica_stack-exported.lei:
[testng] 00:35:17,477 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 00:35:17,478 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:35:17,478 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-01_00-35-17.log]
[testng] 00:35:17,478 |-INFO in ch.qos.logback.core.sift.SiftProcessor@215d4cd1 - End of configuration.
[testng] [2025-01-01 00:35:17,747] [pool-1-thread-3] Initializing /data/michael/2007-01-31_zres_sp2.lei:
[testng] 00:35:17,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 00:35:17,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:35:17,748 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-01_00-35-17.log]
[testng] 00:35:17,749 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f2dc6a1 - End of configuration.
[testng] [2025-01-01 00:35:17,948] [pool-1-thread-2] Initializing /data/julie/c164_1.tif:
[testng] 00:35:17,948 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 00:35:17,948 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:35:17,949 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-01_00-35-17.log]
[testng] 00:35:17,949 |-INFO in ch.qos.logback.core.sift.SiftProcessor@594f2084 - End of configuration.
[testng] [2025-01-01 00:35:20,553] [pool-1-thread-8] Initializing /data/brian/tropo/tropo.lei:
[testng] [2025-01-01 00:35:23,721] [pool-1-thread-1] Initializing /data/christophe/Leica stacks/Nf5.lei:
[testng] [2025-01-01 00:35:25,913] [pool-1-thread-2] Initializing /data/mark/071026-561nm check/071026-561nm check.lei:
[testng] [2025-01-01 00:35:28,965] [pool-1-thread-5] Initializing /data/grant/Leica SP2 (25-11-10).lei:
[testng] [2025-01-01 00:35:29,979] [pool-1-thread-4] Initializing /data/stjude/NIHSSE02-3.lei:
[testng] [2025-01-01 00:35:32,197] [pool-1-thread-3] Initializing /data/matija/PapilioScale40x/PapilioScale40x.lei:
[testng] [2025-01-01 00:35:39,513] [pool-1-thread-8] Initializing /data/andrey/10310500/10310500.lei:
[testng] [2025-01-01 00:36:36,069] [pool-1-thread-4] Initializing /data/christophe/LEI_Saturated_Bug/Saturated_Problem.tif:
[testng] [2025-01-01 00:36:43,668] [pool-1-thread-4] Initializing /data/constantin/cell6/Quant_Image_00.jpg:
[testng] [2025-01-01 00:36:46,024] [pool-1-thread-4] Initializing /data/samples/Leica_sample.lei:
[testng] [2025-01-01 00:36:56,337] [pool-1-thread-4] Initializing /data/constantin/cell6/cell6/Logo.jpg:
[testng] [2025-01-01 00:36:59,233] [pool-1-thread-4] Initializing /data/simon/Leica demo/fish/fish.lei:
[testng] [2025-01-01 00:37:53,196] [pool-1-thread-10] Initializing /data/constantin/cell6/Quant_Image_02.jpg:
[testng] [2025-01-01 00:37:56,658] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6.lei:
[testng] [2025-01-01 00:38:08,302] [pool-1-thread-1] Initializing /data/martin/100422_02-rg-100x_CF1/100422_02-rg-100x_CF1.lei:
[testng] [2025-01-01 00:38:27,293] [pool-1-thread-6] Initializing /data/joel/sequential scan 2/sequential scan 2.lei:
[testng] [2025-01-01 00:39:17,133] [pool-1-thread-3] Initializing /data/constantin/cell6/cell6/Quant_Image_01.jpg:
[testng] [2025-01-01 00:39:19,299] [pool-1-thread-3] Initializing /data/julie/biorad/8291mcd8_raw01.pic:
[testng] [2025-01-01 00:39:27,698] [pool-1-thread-3] Initializing /data/constantin/cell6/Logo.jpg:
[testng] [2025-01-01 00:39:29,397] [pool-1-thread-3] Initializing /data/simon/Leica demo/CFP-DsRed YFP neg/CFP-DsRed YFP neg.lei:
[testng] [2025-01-01 00:40:52,610] [pool-1-thread-7] Initializing /data/christophe/LEI_Saturated_Bug/070123_HippoQ2Q3/Exemple.tif:
[testng] [2025-01-01 00:40:56,733] [pool-1-thread-11] Initializing /data/oliver/o459/o459.lei:
[testng] [2025-01-01 00:41:03,331] [pool-1-thread-7] Initializing /data/david/megan/megan.lei:
[testng] [2025-01-01 00:41:04,913] [pool-1-thread-9] Initializing /data/brian/050627-leica/050628-leica.lei:
[testng] [2025-01-01 00:42:00,095] [pool-1-thread-2] Initializing /data/constantin/cell6/Graphs_1_00.jpg:
[testng] [2025-01-01 00:42:01,944] [pool-1-thread-2] Initializing /data/simon/Leica demo/test/test.lei:
[testng] [2025-01-01 00:42:45,961] [pool-1-thread-5] Initializing /data/berra/eggcmgfp230909/eggcmgfp230909.lei:
[testng] [2025-01-01 00:42:48,768] [pool-1-thread-10] Initializing /data/constantin/cell6/cell6/Quant_Image_02.jpg:
[testng] [2025-01-01 00:42:51,101] [pool-1-thread-10] Initializing /data/vytas/4voxels/4voxels.lei:
[testng] [2025-01-01 00:43:15,688] [pool-1-thread-3] Initializing /data/simon/Leica demo/GFP-YFPcaax/GFP-YFPcaax.lei:
[testng] [2025-01-01 00:43:16,967] [pool-1-thread-6] Initializing /data/clay/leica_stack.tif:
[testng] [2025-01-01 00:43:20,673] [pool-1-thread-6] Initializing /data/constantin/cell6/Quant_Image_01.jpg:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 2332, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 43 minutes 20 seconds
Finished: SUCCESS