Started by upstream project "BIOFORMATS-test-repo" build number 90
originally caused by:
Started by upstream project "Trigger" build number 101
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/jenkins7391526531815547627.sh
+ '[' zip = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_13771_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] 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] 01:23:28,846 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:23:28,848 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service.
[testng] 01:23:28,848 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:23:28,849 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:23:28,849 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:23:28,850 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:23:28,850 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:23:28,850 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:23:28,851 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:23:28,852 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:23:28,852 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:23:28,852 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:23:29,036 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:23:29,036 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:23:29,058 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:23:29,058 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:23:29,067 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:23:29,068 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:23:29,068 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:23:29,068 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:23:29,068 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration.
[testng] 01:23:29,069 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point
[testng] 01:23:29,070 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 219 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-06-12 01:23:29,085] [main] java.version = 17.0.2
[testng] 01:23:29,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:23:29,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:23:29,158 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-12_01-23-29.log]
[testng] 01:23:29,161 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration.
[testng] [2024-06-12 01:23:29,164] [main] testng.directory = /data
[testng] [2024-06-12 01:23:29,164] [main] testng.configDirectory = /config
[testng] [2024-06-12 01:23:29,179] [main] testng.multiplier = 1.0
[testng] [2024-06-12 01:23:29,181] [main] testng.in-memory = false
[testng] [2024-06-12 01:23:29,182] [main] testng.allow-missing = false
[testng] [2024-06-12 01:23:29,182] [main] user.language = en
[testng] [2024-06-12 01:23:29,182] [main] user.country = ${user.country}
[testng] [2024-06-12 01:23:29,182] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-06-12 01:23:29,543] [main] ----------------------------------------
[testng] [2024-06-12 01:23:29,544] [main] Total files: 22
[testng] [2024-06-12 01:23:29,544] [main] Scan time: 0.361 s (16 ms/file)
[testng] [2024-06-12 01:23:29,544] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 22 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-06-12 01:24:09,598] [pool-1-thread-1] Initializing /data/imagej/4D-Stack(256x256x20x10).zip:
[testng] 01:24:09,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:24:09,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:24:09,599 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-12_01-24-09.log]
[testng] 01:24:09,600 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f754f20 - End of configuration.
[testng] [2024-06-12 01:24:14,717] [pool-1-thread-12] Initializing /data/imagej/fat-cells.zip:
[testng] 01:24:14,718 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:24:14,718 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:24:14,719 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-12_01-24-14.log]
[testng] 01:24:14,719 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19b57930 - End of configuration.
[testng] [2024-06-12 01:24:17,107] [pool-1-thread-11] Initializing /data/imagej/FluorescentCells.zip:
[testng] 01:24:17,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:24:17,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:24:17,108 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-12_01-24-17.log]
[testng] 01:24:17,108 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49b5e6bb - End of configuration.
[testng] [2024-06-12 01:24:17,393] [pool-1-thread-10] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip:
[testng] 01:24:17,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:24:17,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:24:17,394 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-12_01-24-17.log]
[testng] 01:24:17,395 |-INFO in ch.qos.logback.core.sift.SiftProcessor@481ffd45 - End of configuration.
[testng] [2024-06-12 01:24:18,665] [pool-1-thread-9] Initializing /data/imagej/xrays.zip:
[testng] 01:24:18,665 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:24:18,665 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:24:18,666 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-12_01-24-18.log]
[testng] 01:24:18,666 |-INFO in ch.qos.logback.core.sift.SiftProcessor@447bc8f9 - End of configuration.
[testng] [2024-06-12 01:24:18,776] [pool-1-thread-8] Initializing /data/imagej/confocal-series.zip:
[testng] 01:24:18,776 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:24:18,776 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:24:18,777 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-12_01-24-18.log]
[testng] 01:24:18,778 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c2eaf8f - End of configuration.
[testng] [2024-06-12 01:24:22,567] [pool-1-thread-7] Initializing /data/imagej/watershed-animation.zip:
[testng] 01:24:22,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:24:22,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:24:22,569 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-12_01-24-22.log]
[testng] 01:24:22,569 |-INFO in ch.qos.logback.core.sift.SiftProcessor@509f50f - End of configuration.
[testng] [2024-06-12 01:24:22,765] [pool-1-thread-6] Initializing /data/imagej/scala-media.zip:
[testng] 01:24:22,765 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:24:22,765 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:24:22,766 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-12_01-24-22.log]
[testng] 01:24:22,766 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4644f4c5 - End of configuration.
[testng] [2024-06-12 01:24:22,882] [pool-1-thread-5] Initializing /data/imagej/m51.zip:
[testng] 01:24:22,882 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:24:22,882 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:24:22,883 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-12_01-24-22.log]
[testng] 01:24:22,884 |-INFO in ch.qos.logback.core.sift.SiftProcessor@487e20d9 - End of configuration.
[testng] [2024-06-12 01:24:23,022] [pool-1-thread-4] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip:
[testng] 01:24:23,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:24:23,023 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:24:23,024 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-12_01-24-23.log]
[testng] 01:24:23,024 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5076499b - End of configuration.
[testng] [2024-06-12 01:24:24,154] [pool-1-thread-3] Initializing /data/imagej/hela-cells.zip:
[testng] 01:24:24,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:24:24,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:24:24,155 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-12_01-24-24.log]
[testng] 01:24:24,155 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75084d66 - End of configuration.
[testng] [2024-06-12 01:24:24,913] [pool-1-thread-2] Initializing /data/samples/bat-cochlea-volume.zip:
[testng] 01:24:24,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:24:24,914 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:24:24,914 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-12_01-24-24.log]
[testng] 01:24:24,915 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3dcf08ec - End of configuration.
[testng] [2024-06-12 01:24:28,324] [pool-1-thread-6] Initializing /data/imagej/RatBrain.zip:
[testng] [2024-06-12 01:24:28,553] [pool-1-thread-9] Initializing /data/imagej/flybrain.zip:
[testng] [2024-06-12 01:24:33,318] [pool-1-thread-5] Initializing /data/imagej/3D_Chromosome.zip:
[testng] [2024-06-12 01:24:35,042] [pool-1-thread-7] Initializing /data/imagej/cheetah_256_8.tif.zip:
[testng] [2024-06-12 01:24:35,775] [pool-1-thread-11] Initializing /data/imagej/gel-electrophoresis.zip:
[testng] [2024-06-12 01:24:38,977] [pool-1-thread-6] Initializing /data/imagej/se3.zip:
[testng] [2024-06-12 01:24:43,286] [pool-1-thread-7] Initializing /data/samples/sdub.zip:
[testng] [2024-06-12 01:24:47,023] [pool-1-thread-5] Initializing /data/imagej/blood-brain-barrier.zip:
[testng] [2024-06-12 01:24:54,508] [pool-1-thread-2] Initializing /data/imagej/mri-stack.zip:
[testng] [2024-06-12 01:24:54,816] [pool-1-thread-7] Initializing /data/imagej/confocal-stack.zip:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1166, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 5 minutes 35 seconds
Finished: SUCCESS