Started by upstream project "BIOFORMATS-test-repo" build number 262
originally caused by:
Started by upstream project "Trigger" build number 286
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8
[BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins15499019738903528260.sh
+ '[' scanr = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_41410_merge_ci -v /uod/idr/repos/curated/scanr:/data -v /uod/idr-scratch/merge-ci/curated/scanr:/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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release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] 04:11:22,435 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 04:11:22,436 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service.
[testng] 04:11:22,436 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 04:11:22,437 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 04:11:22,437 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 04:11:22,437 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 04:11:22,438 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 04:11:22,438 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 04:11:22,438 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 04:11:22,439 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 04:11:22,439 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 04:11:22,439 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 04:11:22,590 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 04:11:22,590 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 04:11:22,616 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 04:11:22,616 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 04:11:22,622 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 04:11:22,623 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 04:11:22,623 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 04:11:22,623 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 04:11:22,623 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration.
[testng] 04:11:22,624 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point
[testng] 04:11:22,624 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 186 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-11-21 04:11:22,633] [main] java.version = 21
[testng] 04:11:22,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 04:11:22,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:11:22,676 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-21_04-11-22.log]
[testng] 04:11:22,677 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration.
[testng] [2024-11-21 04:11:22,679] [main] testng.directory = /data
[testng] [2024-11-21 04:11:22,679] [main] testng.configDirectory = /config
[testng] [2024-11-21 04:11:22,687] [main] testng.multiplier = 1.0
[testng] [2024-11-21 04:11:22,688] [main] testng.in-memory = false
[testng] [2024-11-21 04:11:22,688] [main] testng.allow-missing = false
[testng] [2024-11-21 04:11:22,688] [main] user.language = en
[testng] [2024-11-21 04:11:22,688] [main] user.country = ${user.country}
[testng] [2024-11-21 04:11:22,688] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-11-21 04:15:43,559] [main] ----------------------------------------
[testng] [2024-11-21 04:15:43,559] [main] Total files: 2169
[testng] [2024-11-21 04:15:43,560] [main] Scan time: 260.871 s (120 ms/file)
[testng] [2024-11-21 04:15:43,560] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 17 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-11-21 04:39:27,291] [pool-1-thread-1] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml:
[testng] 04:39:27,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 04:39:27,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:39:27,293 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-21_04-39-27.log]
[testng] 04:39:27,294 |-INFO in ch.qos.logback.core.sift.SiftProcessor@251404ad - End of configuration.
[testng] [2024-11-21 04:40:39,650] [pool-1-thread-12] Initializing /data/ruben/plate_002/experiment_descriptor.xml:
[testng] 04:40:39,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 04:40:39,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:40:39,652 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-21_04-40-39.log]
[testng] 04:40:39,652 |-INFO in ch.qos.logback.core.sift.SiftProcessor@737d2467 - End of configuration.
[testng] [2024-11-21 04:40:43,700] [pool-1-thread-11] Initializing /data/ruben/20100827_004/experiment_descriptor.xml:
[testng] 04:40:43,700 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 04:40:43,700 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:40:43,701 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-21_04-40-43.log]
[testng] 04:40:43,702 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76ed08a2 - End of configuration.
[testng] [2024-11-21 04:43:03,511] [pool-1-thread-10] Initializing /data/gideon/experiment_descriptor.xml:
[testng] 04:43:03,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 04:43:03,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:43:03,512 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-21_04-43-03.log]
[testng] 04:43:03,513 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57dae4d6 - End of configuration.
[testng] [2024-11-21 04:43:37,423] [pool-1-thread-9] Initializing /data/christian/example/experiment_descriptor.xml:
[testng] 04:43:37,424 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 04:43:37,424 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:43:37,425 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-21_04-43-37.log]
[testng] 04:43:37,425 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1efc830f - End of configuration.
[testng] [2024-11-21 04:43:38,821] [pool-1-thread-8] Initializing /data/juergen/Experiment/experiment_descriptor.xml:
[testng] 04:43:38,821 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 04:43:38,821 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:43:38,822 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-21_04-43-38.log]
[testng] 04:43:38,822 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6338a4ea - End of configuration.
[testng] [2024-11-21 04:43:40,338] [pool-1-thread-7] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml:
[testng] 04:43:40,338 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 04:43:40,338 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:43:40,339 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-21_04-43-40.log]
[testng] 04:43:40,339 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53b15750 - End of configuration.
[testng] [2024-11-21 04:46:12,631] [pool-1-thread-6] Initializing /data/embl/Maik_001/experiment_descriptor.xml:
[testng] 04:46:12,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 04:46:12,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:46:12,632 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-21_04-46-12.log]
[testng] 04:46:12,633 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d463720 - End of configuration.
[testng] [2024-11-21 04:46:23,221] [pool-1-thread-5] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml:
[testng] 04:46:23,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 04:46:23,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:46:23,222 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-21_04-46-23.log]
[testng] 04:46:23,222 |-INFO in ch.qos.logback.core.sift.SiftProcessor@510de3be - End of configuration.
[testng] [2024-11-21 04:49:33,884] [pool-1-thread-4] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml:
[testng] 04:49:33,884 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 04:49:33,884 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:49:33,885 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-21_04-49-33.log]
[testng] 04:49:33,885 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e074417 - End of configuration.
[testng] [2024-11-21 04:49:44,430] [pool-1-thread-3] Initializing /data/nadine/experiment_descriptor.xml:
[testng] 04:49:44,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 04:49:44,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:49:44,431 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-21_04-49-44.log]
[testng] 04:49:44,431 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d170371 - End of configuration.
[testng] [2024-11-21 04:49:45,870] [pool-1-thread-2] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml:
[testng] 04:49:45,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 04:49:45,870 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 04:49:45,871 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-21_04-49-45.log]
[testng] 04:49:45,871 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58cb7bf0 - End of configuration.
[testng] [2024-11-21 04:50:43,354] [pool-1-thread-9] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml:
[testng] [2024-11-21 04:54:29,802] [pool-1-thread-8] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml:
[testng] [2024-11-21 04:55:46,675] [pool-1-thread-3] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml:
[testng] [2024-11-21 04:59:43,414] [pool-1-thread-12] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml:
[testng] [2024-11-21 05:01:49,083] [pool-1-thread-6] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml:
[testng] 06:40:08,645 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 06:40:08,645 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:40:08,647 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-21_06-40-08.log]
[testng] 06:40:08,647 |-INFO in ch.qos.logback.core.sift.SiftProcessor@586bbd0a - End of configuration.
[testng] 06:51:08,276 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 06:51:08,276 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:51:08,277 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-21_06-51-08.log]
[testng] 06:51:08,277 |-INFO in ch.qos.logback.core.sift.SiftProcessor@761d4d1b - End of configuration.
[testng] 06:53:14,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 06:53:14,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:53:14,565 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-21_06-53-14.log]
[testng] 06:53:14,565 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68d80eb1 - End of configuration.
[testng] 06:55:44,709 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 06:55:44,709 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:55:44,709 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-21_06-55-44.log]
[testng] 06:55:44,710 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49aa0463 - End of configuration.
[testng] 06:56:30,990 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 06:56:30,990 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 06:56:30,991 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-21_06-56-30.log]
[testng] 06:56:30,991 |-INFO in ch.qos.logback.core.sift.SiftProcessor@434d165f - End of configuration.
[testng] 07:04:23,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 07:04:23,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 07:04:23,550 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-21_07-04-23.log]
[testng] 07:04:23,550 |-INFO in ch.qos.logback.core.sift.SiftProcessor@280b0df9 - End of configuration.
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 901, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 173 minutes 6 seconds
Finished: SUCCESS