Started by upstream project "BIOFORMATS-test-repo" build number 117
originally caused by:
Started by upstream project "Trigger" build number 134
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/jenkins12144230823729720131.sh
+ '[' leica-tcs = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_18320_merge_ci -v /uod/idr/repos/curated/leica-tcs:/data -v /uod/idr-scratch/merge-ci/curated/leica-tcs:/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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release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] 02:34:24,117 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 02:34:24,118 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service.
[testng] 02:34:24,118 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:34:24,120 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:34:24,120 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 02:34:24,120 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 02:34:24,121 |-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] 02:34:24,121 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:34:24,121 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:34:24,122 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 02:34:24,122 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 02:34:24,122 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 02:34:24,399 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 02:34:24,399 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 02:34:24,467 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 02:34:24,467 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 02:34:24,477 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 02:34:24,477 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 02:34:24,477 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 02:34:24,477 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 02:34:24,478 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration.
[testng] 02:34:24,479 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point
[testng] 02:34:24,479 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 358 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-07-11 02:34:24,493] [main] java.version = 21
[testng] 02:34:24,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 02:34:24,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:34:24,574 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-11_02-34-24.log]
[testng] 02:34:24,575 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration.
[testng] [2024-07-11 02:34:24,577] [main] testng.directory = /data
[testng] [2024-07-11 02:34:24,577] [main] testng.configDirectory = /config
[testng] [2024-07-11 02:34:24,630] [main] testng.multiplier = 1.0
[testng] [2024-07-11 02:34:24,631] [main] testng.in-memory = false
[testng] [2024-07-11 02:34:24,631] [main] testng.allow-missing = false
[testng] [2024-07-11 02:34:24,631] [main] user.language = en
[testng] [2024-07-11 02:34:24,631] [main] user.country = ${user.country}
[testng] [2024-07-11 02:34:24,631] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-07-11 02:34:35,430] [main] ----------------------------------------
[testng] [2024-07-11 02:34:35,430] [main] Total files: 944
[testng] [2024-07-11 02:34:35,430] [main] Scan time: 10.799 s (11 ms/file)
[testng] [2024-07-11 02:34:35,431] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 15 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-07-11 02:35:03,964] [pool-1-thread-1] Initializing /data/stjude/AntoDayzerocy3OVP.tif:
[testng] 02:35:03,979 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:35:03,979 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:35:03,981 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-11_02-35-03.log]
[testng] 02:35:03,981 |-INFO in ch.qos.logback.core.sift.SiftProcessor@625d2a8c - End of configuration.
[testng] [2024-07-11 02:35:04,051] [pool-1-thread-12] Initializing /data/brian/Series002_z01.tif:
[testng] 02:35:04,051 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:35:04,051 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:35:04,052 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-11_02-35-04.log]
[testng] 02:35:04,052 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f39ee79 - End of configuration.
[testng] [2024-07-11 02:35:04,085] [pool-1-thread-11] Initializing /data/stjude/Antoday1dblmysglGRP.tif:
[testng] 02:35:04,086 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:35:04,086 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:35:04,086 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-11_02-35-04.log]
[testng] 02:35:04,087 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2207a966 - End of configuration.
[testng] [2024-07-11 02:35:04,127] [pool-1-thread-10] Initializing /data/martin/Series028_z00_ch00.tif:
[testng] 02:35:04,127 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:35:04,127 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:35:04,128 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-11_02-35-04.log]
[testng] 02:35:04,129 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c59eb6d - End of configuration.
[testng] [2024-07-11 02:35:04,176] [pool-1-thread-9] Initializing /data/stjude/AntoDay4dblcatdataGRP.tif:
[testng] 02:35:04,176 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:35:04,176 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:35:04,177 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-11_02-35-04.log]
[testng] 02:35:04,177 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7348a1a1 - End of configuration.
[testng] [2024-07-11 02:35:04,218] [pool-1-thread-8] Initializing /data/brian/Series002_z00_ch00.tif:
[testng] 02:35:04,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:35:04,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:35:04,219 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-11_02-35-04.log]
[testng] 02:35:04,219 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f307cac - End of configuration.
[testng] [2024-07-11 02:35:04,241] [pool-1-thread-7] Initializing /data/primate/Leica_Image.tif:
[testng] 02:35:04,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:35:04,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:35:04,242 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-11_02-35-04.log]
[testng] 02:35:04,242 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3aa073d - End of configuration.
[testng] [2024-07-11 02:35:04,319] [pool-1-thread-6] Initializing /data/stjude/AntoDay4dblmy2GRP.tif:
[testng] 02:35:04,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:35:04,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:35:04,320 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-11_02-35-04.log]
[testng] 02:35:04,320 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d51cc2a - End of configuration.
[testng] [2024-07-11 02:35:04,352] [pool-1-thread-5] Initializing /data/dave/series 35/042911_Series035_t00_z000_ch00.tif:
[testng] 02:35:04,353 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:35:04,353 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:35:04,353 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-11_02-35-04.log]
[testng] 02:35:04,354 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7844693b - End of configuration.
[testng] [2024-07-11 02:35:09,140] [pool-1-thread-4] Initializing /data/stjude/AntoDay4dblmyGRP.tif:
[testng] 02:35:09,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:35:09,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:35:09,141 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-11_02-35-09.log]
[testng] 02:35:09,141 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b894ba5 - End of configuration.
[testng] [2024-07-11 02:35:09,182] [pool-1-thread-3] Initializing /data/stjude/AntoDayzerocy3GRP.tif:
[testng] 02:35:09,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:35:09,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:35:09,183 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-11_02-35-09.log]
[testng] 02:35:09,183 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dc10141 - End of configuration.
[testng] [2024-07-11 02:35:09,211] [pool-1-thread-2] Initializing /data/stjude/AntoDay1dblGRP.tif:
[testng] 02:35:09,211 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:35:09,211 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:35:09,212 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-11_02-35-09.log]
[testng] 02:35:09,212 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76920921 - End of configuration.
[testng] [2024-07-11 02:35:12,171] [pool-1-thread-1] Initializing /data/stjude/AntoDay1cy3/c01f0001.TIF:
[testng] [2024-07-11 02:35:12,194] [pool-1-thread-4] Initializing /data/stjude/Antoday1dblcatsglGRP.tif:
[testng] [2024-07-11 02:35:12,224] [pool-1-thread-7] Initializing /data/stjude/Antoday1dblcat2dataGRP.tif:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 795, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 9 minutes 44 seconds
Finished: SUCCESS