Started by upstream project "BIOFORMATS-test-repo" build number 293
originally caused by:
Started by upstream project "Trigger" build number 312
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9
[BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins16177082398818523774.sh
+ '[' zip = slidebook ']'
++ date +%u
+ '[' 2 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_46264_merge_ci -v /uod/idr/repos/curated/zip:/data -v /uod/idr-scratch/merge-ci/curated/zip:/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] WARNING: An illegal reflective access operation has occurred
[testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket
[testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener
[testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
[testng] WARNING: All illegal access operations will be denied in a future release
[testng] File leak detector installed
[testng] 00:34:10,752 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 00:34:10,753 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service.
[testng] 00:34:10,753 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:34:10,754 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:34:10,755 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 00:34:10,755 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 00:34:10,755 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 00:34:10,755 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:34:10,756 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:34:10,756 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 00:34:10,757 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 00:34:10,757 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 00:34:10,919 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 00:34:10,919 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 00:34:10,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 00:34:10,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 00:34:10,946 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 00:34:10,946 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 00:34:10,946 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 00:34:10,946 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 00:34:10,946 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration.
[testng] 00:34:10,947 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point
[testng] 00:34:10,947 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 191 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-12-17 00:34:10,955] [main] java.version = 11.0.16
[testng] 00:34:10,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 00:34:10,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:34:10,999 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-17_00-34-10.log]
[testng] 00:34:11,001 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration.
[testng] [2024-12-17 00:34:11,003] [main] testng.directory = /data
[testng] [2024-12-17 00:34:11,003] [main] testng.configDirectory = /config
[testng] [2024-12-17 00:34:11,012] [main] testng.multiplier = 1.0
[testng] [2024-12-17 00:34:11,013] [main] testng.in-memory = false
[testng] [2024-12-17 00:34:11,014] [main] testng.allow-missing = false
[testng] [2024-12-17 00:34:11,014] [main] user.language = en
[testng] [2024-12-17 00:34:11,014] [main] user.country = ${user.country}
[testng] [2024-12-17 00:34:11,014] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-12-17 00:34:11,885] [main] ----------------------------------------
[testng] [2024-12-17 00:34:11,885] [main] Total files: 22
[testng] [2024-12-17 00:34:11,885] [main] Scan time: 0.871 s (39 ms/file)
[testng] [2024-12-17 00:34:11,885] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 22 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-12-17 00:38:42,144] [pool-1-thread-1] Initializing /data/imagej/confocal-series.zip:
[testng] 00:38:42,144 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 00:38:42,145 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:38:42,146 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-17_00-38-42.log]
[testng] 00:38:42,147 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52f1b8d5 - End of configuration.
[testng] [2024-12-17 00:38:56,232] [pool-1-thread-12] Initializing /data/imagej/xrays.zip:
[testng] 00:38:56,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 00:38:56,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:38:56,234 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-17_00-38-56.log]
[testng] 00:38:56,234 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5bfb7450 - End of configuration.
[testng] [2024-12-17 00:39:01,683] [pool-1-thread-11] Initializing /data/imagej/fat-cells.zip:
[testng] 00:39:01,683 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 00:39:01,683 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:39:01,684 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-17_00-39-01.log]
[testng] 00:39:01,684 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64ee74a4 - End of configuration.
[testng] [2024-12-17 00:39:09,999] [pool-1-thread-10] Initializing /data/imagej/confocal-stack.zip:
[testng] 00:39:10,000 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 00:39:10,000 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:39:10,000 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-17_00-39-10.log]
[testng] 00:39:10,001 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1faa2417 - End of configuration.
[testng] [2024-12-17 00:39:30,857] [pool-1-thread-9] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip:
[testng] 00:39:30,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 00:39:30,857 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:39:30,857 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-17_00-39-30.log]
[testng] 00:39:30,858 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dd62a96 - End of configuration.
[testng] [2024-12-17 00:39:46,657] [pool-1-thread-8] Initializing /data/imagej/m51.zip:
[testng] 00:39:46,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 00:39:46,658 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:39:46,658 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-17_00-39-46.log]
[testng] 00:39:46,658 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2750c33 - End of configuration.
[testng] [2024-12-17 00:39:53,011] [pool-1-thread-7] Initializing /data/imagej/cheetah_256_8.tif.zip:
[testng] 00:39:53,012 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 00:39:53,012 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:39:53,012 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-17_00-39-53.log]
[testng] 00:39:53,013 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32e5bb33 - End of configuration.
[testng] [2024-12-17 00:40:07,652] [pool-1-thread-6] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip:
[testng] 00:40:07,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 00:40:07,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:40:07,653 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-17_00-40-07.log]
[testng] 00:40:07,653 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1995b358 - End of configuration.
[testng] [2024-12-17 00:40:19,280] [pool-1-thread-5] Initializing /data/imagej/flybrain.zip:
[testng] 00:40:19,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 00:40:19,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:40:19,281 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-17_00-40-19.log]
[testng] 00:40:19,281 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24819205 - End of configuration.
[testng] [2024-12-17 00:40:39,619] [pool-1-thread-4] Initializing /data/imagej/RatBrain.zip:
[testng] 00:40:39,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 00:40:39,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:40:39,620 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-17_00-40-39.log]
[testng] 00:40:39,621 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b0ca4ce - End of configuration.
[testng] [2024-12-17 00:40:47,520] [pool-1-thread-3] Initializing /data/imagej/3D_Chromosome.zip:
[testng] 00:40:47,520 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 00:40:47,520 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:40:47,521 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-17_00-40-47.log]
[testng] 00:40:47,521 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c989f40 - End of configuration.
[testng] [2024-12-17 00:40:55,399] [pool-1-thread-2] Initializing /data/imagej/se3.zip:
[testng] 00:40:55,399 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 00:40:55,399 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:40:55,400 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-17_00-40-55.log]
[testng] 00:40:55,400 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f31f5df - End of configuration.
[testng] [2024-12-17 00:42:41,756] [pool-1-thread-8] Initializing /data/samples/sdub.zip:
[testng] [2024-12-17 00:42:44,096] [pool-1-thread-12] Initializing /data/imagej/scala-media.zip:
[testng] [2024-12-17 00:43:22,447] [pool-1-thread-3] Initializing /data/imagej/watershed-animation.zip:
[testng] [2024-12-17 00:43:31,163] [pool-1-thread-4] Initializing /data/imagej/gel-electrophoresis.zip:
[testng] [2024-12-17 00:43:42,003] [pool-1-thread-8] Initializing /data/imagej/hela-cells.zip:
[testng] [2024-12-17 00:44:01,563] [pool-1-thread-7] Initializing /data/samples/bat-cochlea-volume.zip:
[testng] [2024-12-17 00:44:54,443] [pool-1-thread-11] Initializing /data/imagej/FluorescentCells.zip:
[testng] [2024-12-17 00:45:04,354] [pool-1-thread-9] Initializing /data/imagej/4D-Stack(256x256x20x10).zip:
[testng] [2024-12-17 00:45:24,147] [pool-1-thread-12] Initializing /data/imagej/mri-stack.zip:
[testng] [2024-12-17 00:45:29,634] [pool-1-thread-6] Initializing /data/imagej/blood-brain-barrier.zip:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1166, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 19 minutes 57 seconds
Finished: SUCCESS