Started by upstream project "BIOFORMATS-test-repo" build number 37
originally caused by:
Started by upstream project "Trigger" build number 42
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5
[BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins6914560124331527749.sh
+ '[' scanr = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_5182_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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release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] 02:14:18,843 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 02:14:18,844 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service.
[testng] 02:14:18,844 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:14:18,845 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:14:18,846 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 02:14:18,846 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 02:14:18,846 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 02:14:18,846 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:14:18,847 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:14:18,848 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 02:14:18,848 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 02:14:18,848 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 02:14:19,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 02:14:19,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 02:14:19,064 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 02:14:19,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 02:14:19,074 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 02:14:19,074 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 02:14:19,075 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 02:14:19,075 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 02:14:19,075 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration.
[testng] 02:14:19,076 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point
[testng] 02:14:19,076 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 229 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-04-18 02:14:19,094] [main] java.version = 21
[testng] 02:14:19,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 02:14:19,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:14:19,157 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-18_02-14-19.log]
[testng] 02:14:19,159 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration.
[testng] [2024-04-18 02:14:19,161] [main] testng.directory = /data
[testng] [2024-04-18 02:14:19,161] [main] testng.configDirectory = /config
[testng] [2024-04-18 02:14:19,177] [main] testng.multiplier = 1.0
[testng] [2024-04-18 02:14:19,178] [main] testng.in-memory = false
[testng] [2024-04-18 02:14:19,178] [main] testng.allow-missing = false
[testng] [2024-04-18 02:14:19,178] [main] user.language = en
[testng] [2024-04-18 02:14:19,178] [main] user.country = ${user.country}
[testng] [2024-04-18 02:14:19,178] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-04-18 02:19:36,293] [main] ----------------------------------------
[testng] [2024-04-18 02:19:36,294] [main] Total files: 2169
[testng] [2024-04-18 02:19:36,294] [main] Scan time: 317.115 s (146 ms/file)
[testng] [2024-04-18 02:19:36,295] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 17 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-04-18 02:36:44,198] [pool-1-thread-1] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml:
[testng] 02:36:44,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:36:44,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:36:44,200 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-18_02-36-44.log]
[testng] 02:36:44,201 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1cf9ffa - End of configuration.
[testng] [2024-04-18 02:37:17,707] [pool-1-thread-12] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml:
[testng] 02:37:17,708 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:37:17,708 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:37:17,709 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-18_02-37-17.log]
[testng] 02:37:17,710 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61d952ca - End of configuration.
[testng] [2024-04-18 02:39:08,441] [pool-1-thread-11] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml:
[testng] 02:39:08,441 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:39:08,442 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:39:08,443 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-18_02-39-08.log]
[testng] 02:39:08,444 |-INFO in ch.qos.logback.core.sift.SiftProcessor@790ef9ee - End of configuration.
[testng] [2024-04-18 02:42:33,525] [pool-1-thread-10] Initializing /data/nadine/experiment_descriptor.xml:
[testng] 02:42:33,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:42:33,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:42:33,527 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-18_02-42-33.log]
[testng] 02:42:33,528 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22bea41 - End of configuration.
[testng] [2024-04-18 02:42:33,878] [pool-1-thread-9] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml:
[testng] 02:42:33,878 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:42:33,878 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:42:33,879 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-18_02-42-33.log]
[testng] 02:42:33,879 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64fc1f59 - End of configuration.
[testng] [2024-04-18 02:42:41,523] [pool-1-thread-8] Initializing /data/ruben/20100827_004/experiment_descriptor.xml:
[testng] 02:42:41,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:42:41,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:42:41,524 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-18_02-42-41.log]
[testng] 02:42:41,524 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4894a29a - End of configuration.
[testng] [2024-04-18 02:45:27,158] [pool-1-thread-7] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml:
[testng] 02:45:27,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:45:27,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:45:27,160 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-18_02-45-27.log]
[testng] 02:45:27,160 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6718173a - End of configuration.
[testng] [2024-04-18 02:46:38,773] [pool-1-thread-6] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml:
[testng] 02:46:38,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:46:38,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:46:38,775 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-18_02-46-38.log]
[testng] 02:46:38,775 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51b7fbfa - End of configuration.
[testng] [2024-04-18 02:46:52,833] [pool-1-thread-5] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml:
[testng] 02:46:52,833 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:46:52,833 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:46:52,834 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-18_02-46-52.log]
[testng] 02:46:52,835 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d431695 - End of configuration.
[testng] [2024-04-18 02:47:48,000] [pool-1-thread-4] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml:
[testng] 02:47:48,000 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:47:48,000 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:47:48,002 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-18_02-47-48.log]
[testng] 02:47:48,002 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3be774f1 - End of configuration.
[testng] [2024-04-18 02:50:56,125] [pool-1-thread-3] Initializing /data/ruben/plate_002/experiment_descriptor.xml:
[testng] 02:50:56,126 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:50:56,126 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:50:56,127 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-18_02-50-56.log]
[testng] 02:50:56,128 |-INFO in ch.qos.logback.core.sift.SiftProcessor@712c9e82 - End of configuration.
[testng] [2024-04-18 02:50:59,694] [pool-1-thread-2] Initializing /data/embl/Maik_001/experiment_descriptor.xml:
[testng] 02:50:59,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:50:59,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:50:59,695 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-18_02-50-59.log]
[testng] 02:50:59,696 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57cc9fff - End of configuration.
[testng] [2024-04-18 02:51:12,548] [pool-1-thread-10] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml:
[testng] [2024-04-18 02:52:27,286] [pool-1-thread-9] Initializing /data/christian/example/experiment_descriptor.xml:
[testng] [2024-04-18 02:52:28,699] [pool-1-thread-9] Initializing /data/gideon/experiment_descriptor.xml:
[testng] [2024-04-18 02:53:03,776] [pool-1-thread-3] Initializing /data/juergen/Experiment/experiment_descriptor.xml:
[testng] [2024-04-18 02:53:06,083] [pool-1-thread-3] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 901, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 45 minutes 10 seconds
Finished: SUCCESS