Started by upstream project "BIOFORMATS-test-repo" build number 194
originally caused by:
Started by user devspace
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@10
[BIOFORMATS-test-folder@10] $ /bin/bash -xe /tmp/jenkins5810359540006747982.sh
+ '[' zip = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_30670_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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release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] 11:03:30,941 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 11:03:30,943 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service.
[testng] 11:03:30,943 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 11:03:30,944 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 11:03:30,944 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 11:03:30,945 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 11:03:30,945 |-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] 11:03:30,945 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 11:03:30,946 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 11:03:30,947 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 11:03:30,947 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 11:03:30,948 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 11:03:31,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 11:03:31,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 11:03:31,148 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 11:03:31,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 11:03:31,155 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 11:03:31,156 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 11:03:31,156 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 11:03:31,156 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 11:03:31,156 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration.
[testng] 11:03:31,157 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point
[testng] 11:03:31,157 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 211 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-09-19 11:03:31,166] [main] java.version = 21
[testng] 11:03:31,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 11:03:31,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:03:31,212 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-19_11-03-31.log]
[testng] 11:03:31,214 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration.
[testng] [2024-09-19 11:03:31,215] [main] testng.directory = /data
[testng] [2024-09-19 11:03:31,216] [main] testng.configDirectory = /config
[testng] [2024-09-19 11:03:31,225] [main] testng.multiplier = 1.0
[testng] [2024-09-19 11:03:31,225] [main] testng.in-memory = false
[testng] [2024-09-19 11:03:31,225] [main] testng.allow-missing = false
[testng] [2024-09-19 11:03:31,225] [main] user.language = en
[testng] [2024-09-19 11:03:31,225] [main] user.country = ${user.country}
[testng] [2024-09-19 11:03:31,225] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-09-19 11:03:32,119] [main] ----------------------------------------
[testng] [2024-09-19 11:03:32,119] [main] Total files: 22
[testng] [2024-09-19 11:03:32,119] [main] Scan time: 0.894 s (40 ms/file)
[testng] [2024-09-19 11:03:32,120] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 22 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-09-19 11:06:25,684] [pool-1-thread-1] Initializing /data/imagej/Rat_Hippocampal_Neuron.zip:
[testng] 11:06:25,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 11:06:25,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:06:25,687 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-19_11-06-25.log]
[testng] 11:06:25,688 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67e2af77 - End of configuration.
[testng] [2024-09-19 11:06:31,680] [pool-1-thread-12] Initializing /data/imagej/watershed-animation.zip:
[testng] 11:06:31,680 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 11:06:31,680 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:06:31,681 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-19_11-06-31.log]
[testng] 11:06:31,681 |-INFO in ch.qos.logback.core.sift.SiftProcessor@289b666f - End of configuration.
[testng] [2024-09-19 11:06:34,835] [pool-1-thread-11] Initializing /data/imagej/cheetah_256_8.tif.zip:
[testng] 11:06:34,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 11:06:34,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:06:34,836 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-19_11-06-34.log]
[testng] 11:06:34,837 |-INFO in ch.qos.logback.core.sift.SiftProcessor@124b54a8 - End of configuration.
[testng] [2024-09-19 11:06:39,041] [pool-1-thread-10] Initializing /data/imagej/Rat_Hippocampal_Neuron2.zip:
[testng] 11:06:39,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 11:06:39,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:06:39,043 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-19_11-06-39.log]
[testng] 11:06:39,043 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e5c83f0 - End of configuration.
[testng] [2024-09-19 11:06:44,997] [pool-1-thread-9] Initializing /data/imagej/mri-stack.zip:
[testng] 11:06:44,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 11:06:44,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:06:44,999 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-19_11-06-44.log]
[testng] 11:06:44,999 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34408473 - End of configuration.
[testng] [2024-09-19 11:06:48,813] [pool-1-thread-8] Initializing /data/imagej/gel-electrophoresis.zip:
[testng] 11:06:48,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 11:06:48,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:06:48,814 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-19_11-06-48.log]
[testng] 11:06:48,814 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72ab1e71 - End of configuration.
[testng] [2024-09-19 11:06:53,965] [pool-1-thread-7] Initializing /data/imagej/3D_Chromosome.zip:
[testng] 11:06:53,966 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 11:06:53,966 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:06:53,966 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-19_11-06-53.log]
[testng] 11:06:53,967 |-INFO in ch.qos.logback.core.sift.SiftProcessor@373b5721 - End of configuration.
[testng] [2024-09-19 11:06:57,449] [pool-1-thread-6] Initializing /data/imagej/hela-cells.zip:
[testng] 11:06:57,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 11:06:57,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:06:57,450 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-19_11-06-57.log]
[testng] 11:06:57,450 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a30a3b6 - End of configuration.
[testng] [2024-09-19 11:07:01,920] [pool-1-thread-5] Initializing /data/imagej/FluorescentCells.zip:
[testng] 11:07:01,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 11:07:01,921 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:07:01,921 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-19_11-07-01.log]
[testng] 11:07:01,922 |-INFO in ch.qos.logback.core.sift.SiftProcessor@309cd7df - End of configuration.
[testng] [2024-09-19 11:07:05,748] [pool-1-thread-4] Initializing /data/imagej/flybrain.zip:
[testng] 11:07:05,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 11:07:05,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:07:05,749 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-19_11-07-05.log]
[testng] 11:07:05,749 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7980cd53 - End of configuration.
[testng] [2024-09-19 11:07:18,194] [pool-1-thread-3] Initializing /data/imagej/4D-Stack(256x256x20x10).zip:
[testng] 11:07:18,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 11:07:18,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:07:18,196 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-19_11-07-18.log]
[testng] 11:07:18,196 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1dd80ae9 - End of configuration.
[testng] [2024-09-19 11:07:31,191] [pool-1-thread-2] Initializing /data/imagej/xrays.zip:
[testng] 11:07:31,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 11:07:31,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 11:07:31,192 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-19_11-07-31.log]
[testng] 11:07:31,192 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45749ad8 - End of configuration.
[testng] [2024-09-19 11:08:10,953] [pool-1-thread-2] Initializing /data/imagej/confocal-series.zip:
[testng] [2024-09-19 11:08:29,523] [pool-1-thread-12] Initializing /data/samples/bat-cochlea-volume.zip:
[testng] [2024-09-19 11:08:35,267] [pool-1-thread-9] Initializing /data/imagej/RatBrain.zip:
[testng] [2024-09-19 11:08:39,238] [pool-1-thread-7] Initializing /data/imagej/confocal-stack.zip:
[testng] [2024-09-19 11:08:53,830] [pool-1-thread-5] Initializing /data/imagej/scala-media.zip:
[testng] [2024-09-19 11:08:57,414] [pool-1-thread-11] Initializing /data/imagej/m51.zip:
[testng] [2024-09-19 11:09:22,695] [pool-1-thread-6] Initializing /data/imagej/blood-brain-barrier.zip:
[testng] [2024-09-19 11:09:36,594] [pool-1-thread-1] Initializing /data/imagej/se3.zip:
[testng] [2024-09-19 11:09:48,677] [pool-1-thread-10] Initializing /data/samples/sdub.zip:
[testng] [2024-09-19 11:09:53,433] [pool-1-thread-9] Initializing /data/imagej/fat-cells.zip:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1166, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 11 minutes 54 seconds
Finished: SUCCESS