Started by upstream project "BIOFORMATS-test-repo" build number 28
originally caused by:
Started by upstream project "Trigger" build number 31
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4
[BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins4485581421517252812.sh
+ '[' imaris = slidebook ']'
++ date +%u
+ '[' 2 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_3697_merge_ci -v /uod/idr/repos/curated/imaris:/data -v /uod/idr-scratch/merge-ci/curated/imaris:/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] 02:17:02,679 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 02:17:02,681 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service.
[testng] 02:17:02,681 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:17:02,682 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:17:02,682 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 02:17:02,683 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 02:17:02,683 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 02:17:02,683 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:17:02,683 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:17:02,684 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 02:17:02,684 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 02:17:02,685 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 02:17:02,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 02:17:02,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 02:17:02,884 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 02:17:02,884 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 02:17:02,889 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 02:17:02,889 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 02:17:02,889 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 02:17:02,890 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 02:17:02,890 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration.
[testng] 02:17:02,890 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point
[testng] 02:17:02,891 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 208 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-04-09 02:17:02,900] [main] java.version = 11.0.16
[testng] 02:17:02,903 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 02:17:02,903 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:02,945 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-09_02-17-02.log]
[testng] 02:17:02,947 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
[testng] [2024-04-09 02:17:02,949] [main] testng.directory = /data
[testng] [2024-04-09 02:17:02,949] [main] testng.configDirectory = /config
[testng] [2024-04-09 02:17:02,960] [main] testng.multiplier = 1.0
[testng] [2024-04-09 02:17:02,961] [main] testng.in-memory = false
[testng] [2024-04-09 02:17:02,961] [main] testng.allow-missing = false
[testng] [2024-04-09 02:17:02,961] [main] user.language = en
[testng] [2024-04-09 02:17:02,961] [main] user.country = ${user.country}
[testng] [2024-04-09 02:17:02,961] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-04-09 02:17:09,768] [main] ----------------------------------------
[testng] [2024-04-09 02:17:09,768] [main] Total files: 67
[testng] [2024-04-09 02:17:09,768] [main] Scan time: 6.806 s (101 ms/file)
[testng] [2024-04-09 02:17:09,768] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 59 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-04-09 02:17:32,841] [pool-1-thread-1] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal_IMS3.ims:
[testng] 02:17:32,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:17:32,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:32,845 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-09_02-17-32.log]
[testng] 02:17:32,845 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6227f740 - End of configuration.
[testng] [2024-04-09 02:17:32,896] [pool-1-thread-12] Initializing /data/generated/10-31_E_t0001.ims:
[testng] 02:17:32,896 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:17:32,896 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:32,899 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-09_02-17-32.log]
[testng] 02:17:32,899 |-INFO in ch.qos.logback.core.sift.SiftProcessor@bf95aef - End of configuration.
[testng] [2024-04-09 02:17:32,925] [pool-1-thread-11] Initializing /data/jake/p75Cherry M2 010-3~B.ims:
[testng] 02:17:32,926 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:17:32,926 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:32,927 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-09_02-17-32.log]
[testng] 02:17:32,928 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d49f5b2 - End of configuration.
[testng] [2024-04-09 02:17:32,973] [pool-1-thread-10] Initializing /data/generated/10-31_E_t0013.ims:
[testng] 02:17:32,974 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:17:32,974 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:32,975 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-09_02-17-32.log]
[testng] 02:17:32,975 |-INFO in ch.qos.logback.core.sift.SiftProcessor@550259ed - End of configuration.
[testng] [2024-04-09 02:17:33,015] [pool-1-thread-9] Initializing /data/james/apoEcherry_IL10GFP_tfn647_1_R3D_D3D-Display Adjustment-Save-2011-7-5-1.ims:
[testng] 02:17:33,016 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:17:33,016 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:33,017 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-09_02-17-33.log]
[testng] 02:17:33,017 |-INFO in ch.qos.logback.core.sift.SiftProcessor@582a05f9 - End of configuration.
[testng] [2024-04-09 02:17:33,067] [pool-1-thread-8] Initializing /data/generated/10-31_E_t0000.ims:
[testng] 02:17:33,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:17:33,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:33,068 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-09_02-17-33.log]
[testng] 02:17:33,069 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45295425 - End of configuration.
[testng] [2024-04-09 02:17:33,089] [pool-1-thread-7] Initializing /data/jason/imaris_5_5_demoimages/HeLaCell.ims:
[testng] 02:17:33,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:17:33,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:33,091 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-09_02-17-33.log]
[testng] 02:17:33,091 |-INFO in ch.qos.logback.core.sift.SiftProcessor@595d55e4 - End of configuration.
[testng] [2024-04-09 02:17:33,148] [pool-1-thread-6] Initializing /data/public/davemason/TransFactors_2C_34Z_SRRF_IMS3.ims:
[testng] 02:17:33,148 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:17:33,148 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:33,149 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-09_02-17-33.log]
[testng] 02:17:33,150 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9c0eaa3 - End of configuration.
[testng] [2024-04-09 02:17:33,188] [pool-1-thread-5] Initializing /data/jason/imaris_5_5_demoimages/PlantCell.ims:
[testng] 02:17:33,188 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:17:33,188 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:33,189 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-09_02-17-33.log]
[testng] 02:17:33,189 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a3bb633 - End of configuration.
[testng] [2024-04-09 02:17:33,285] [pool-1-thread-4] Initializing /data/niko/imaris-testfile_5x5x5.ims:
[testng] 02:17:33,286 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:17:33,286 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:33,287 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-09_02-17-33.log]
[testng] 02:17:33,288 |-INFO in ch.qos.logback.core.sift.SiftProcessor@738e4b6 - End of configuration.
[testng] [2024-04-09 02:17:33,304] [pool-1-thread-3] Initializing /data/qa-17839/Fusion _Stack.ims:
[testng] 02:17:33,304 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:17:33,304 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:33,305 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-09_02-17-33.log]
[testng] 02:17:33,306 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ae741b2 - End of configuration.
[testng] [2024-04-09 02:17:33,357] [pool-1-thread-2] Initializing /data/public/eliana/retina_large.ims:
[testng] 02:17:33,357 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:17:33,357 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:17:33,358 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-09_02-17-33.log]
[testng] 02:17:33,359 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48508d79 - End of configuration.
[testng] [2024-04-09 02:17:35,066] [pool-1-thread-4] Initializing /data/public/davemason/Convallaria_3C_1T_2x2grid_confocal_IMS3.ims:
[testng] [2024-04-09 02:17:35,091] [pool-1-thread-10] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal.ims:
[testng] [2024-04-09 02:17:35,125] [pool-1-thread-12] Initializing /data/generated/10-31_E_t0006.ims:
[testng] [2024-04-09 02:17:35,141] [pool-1-thread-8] Initializing /data/generated/mri-stack-original.ims:
[testng] [2024-04-09 02:17:35,152] [pool-1-thread-7] Initializing /data/qa-8019/wrong_num_dimensions.ims:
[testng] [2024-04-09 02:17:35,501] [pool-1-thread-8] Initializing /data/public/davemason/Convallaria_3C_3T_2x2grid_confocal.ims:
[testng] [2024-04-09 02:17:35,650] [pool-1-thread-12] Initializing /data/public/davemason/TransFactors_2C_SRRF_IMS3.ims:
[testng] [2024-04-09 02:17:35,855] [pool-1-thread-5] Initializing /data/public/davemason/Convallaria_3C_10T_confocal.ims:
[testng] [2024-04-09 02:17:36,137] [pool-1-thread-9] Initializing /data/generated/10-31_E_t0009.ims:
[testng] [2024-04-09 02:17:36,192] [pool-1-thread-7] Initializing /data/public/davemason/Convallaria_3C_1T_confocal_IMS3.ims:
[testng] [2024-04-09 02:17:36,449] [pool-1-thread-9] Initializing /data/oliver/Stack2_float32Bit.ims:
[testng] [2024-04-09 02:17:36,529] [pool-1-thread-1] Initializing /data/generated/10-31_E_t0002.ims:
[testng] [2024-04-09 02:17:36,844] [pool-1-thread-1] Initializing /data/qa-17522/2016-07-26_17.11.03_Sample Prefix_5P298C2_Protocol.ims:
[testng] [2024-04-09 02:17:36,911] [pool-1-thread-5] Initializing /data/jason/imaris_5_5_demoimages/PtK2Cell.ims:
[testng] [2024-04-09 02:17:37,011] [pool-1-thread-10] Initializing /data/generated/10-31_E_t0007.ims:
BUILD SUCCESSFUL
Total time: 2 minutes 16 seconds
Finished: SUCCESS