Started by upstream project "BIOFORMATS-test-repo" build number 214
originally caused by:
Started by upstream project "Trigger" build number 241
originally caused by:
Started by user devspace
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/jenkins5567886742973917463.sh
+ '[' amira = slidebook ']'
++ date +%u
+ '[' 2 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_33952_merge_ci -v /uod/idr/repos/curated/amira:/data -v /uod/idr-scratch/merge-ci/curated/amira:/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] 08:49:12,060 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 08:49:12,061 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service.
[testng] 08:49:12,061 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 08:49:12,062 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 08:49:12,063 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 08:49:12,063 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 08:49:12,063 |-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] 08:49:12,063 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 08:49:12,064 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 08:49:12,064 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 08:49:12,065 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 08:49:12,065 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 08:49:12,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 08:49:12,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 08:49:12,260 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 08:49:12,260 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 08:49:12,265 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 08:49:12,265 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 08:49:12,265 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 08:49:12,266 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 08:49:12,266 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration.
[testng] 08:49:12,266 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point
[testng] 08:49:12,266 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 202 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-10-08 08:49:12,275] [main] java.version = 11.0.16
[testng] 08:49:12,278 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 08:49:12,278 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:49:12,340 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-08_08-49-12.log]
[testng] 08:49:12,342 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration.
[testng] [2024-10-08 08:49:12,345] [main] testng.directory = /data
[testng] [2024-10-08 08:49:12,345] [main] testng.configDirectory = /config
[testng] [2024-10-08 08:49:12,358] [main] testng.multiplier = 1.0
[testng] [2024-10-08 08:49:12,360] [main] testng.in-memory = false
[testng] [2024-10-08 08:49:12,361] [main] testng.allow-missing = false
[testng] [2024-10-08 08:49:12,361] [main] user.language = en
[testng] [2024-10-08 08:49:12,361] [main] user.country = ${user.country}
[testng] [2024-10-08 08:49:12,361] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-10-08 08:49:16,976] [main] ----------------------------------------
[testng] [2024-10-08 08:49:16,977] [main] Total files: 15
[testng] [2024-10-08 08:49:16,977] [main] Scan time: 4.615 s (307 ms/file)
[testng] [2024-10-08 08:49:16,977] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 12 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-10-08 08:49:26,928] [pool-1-thread-1] Initializing /data/jeremy/Hiv_spikes.am:
[testng] 08:49:26,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 08:49:26,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:49:26,932 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-08_08-49-26.log]
[testng] 08:49:26,932 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15194bc2 - End of configuration.
[testng] [2024-10-08 08:49:27,340] [pool-1-thread-12] Initializing /data/public/imagesc-50585/BF_CheckMIB.am:
[testng] 08:49:27,341 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 08:49:27,341 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:49:27,342 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-08_08-49-27.log]
[testng] 08:49:27,343 |-INFO in ch.qos.logback.core.sift.SiftProcessor@282b7618 - End of configuration.
[testng] [2024-10-08 08:49:27,749] [pool-1-thread-11] Initializing /data/samples/emptykey/test.am:
[testng] 08:49:27,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 08:49:27,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:49:27,751 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-08_08-49-27.log]
[testng] 08:49:27,751 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ea0c1f0 - End of configuration.
[testng] [2024-10-08 08:49:28,150] [pool-1-thread-10] Initializing /data/jeremy/Virus_Membrane7-screenshot.PNG:
[testng] 08:49:28,150 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 08:49:28,150 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:49:28,151 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-08_08-49-28.log]
[testng] 08:49:28,151 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e1e360c - End of configuration.
[testng] [2024-10-08 08:49:28,181] [pool-1-thread-9] Initializing /data/public/imagesc-50585/BF_Check.tif:
[testng] 08:49:28,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 08:49:28,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:49:28,182 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-08_08-49-28.log]
[testng] 08:49:28,182 |-INFO in ch.qos.logback.core.sift.SiftProcessor@525738bb - End of configuration.
[testng] [2024-10-08 08:49:29,232] [pool-1-thread-8] Initializing /data/ilya/test.am:
[testng] 08:49:29,233 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 08:49:29,233 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:49:29,233 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-08_08-49-29.log]
[testng] 08:49:29,234 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7426236b - End of configuration.
[testng] [2024-10-08 08:49:29,687] [pool-1-thread-7] Initializing /data/public/imagesc-50585/BF_CheckAmira.am:
[testng] 08:49:29,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 08:49:29,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:49:29,688 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-08_08-49-29.log]
[testng] 08:49:29,688 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d515d6a - End of configuration.
[testng] [2024-10-08 08:49:30,183] [pool-1-thread-6] Initializing /data/johannes/template.grey:
[testng] 08:49:30,184 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 08:49:30,184 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:49:30,184 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-08_08-49-30.log]
[testng] 08:49:30,184 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a3941ab - End of configuration.
[testng] [2024-10-08 08:49:30,619] [pool-1-thread-5] Initializing /data/jcb/201108088/Haberman-Fig4A-original.am:
[testng] 08:49:30,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 08:49:30,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:49:30,619 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-08_08-49-30.log]
[testng] 08:49:30,620 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2aead771 - End of configuration.
[testng] [2024-10-08 08:49:31,063] [pool-1-thread-4] Initializing /data/jeremy/Virus_Membrane7.am:
[testng] 08:49:31,063 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 08:49:31,064 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:49:31,064 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-08_08-49-31.log]
[testng] 08:49:31,065 |-INFO in ch.qos.logback.core.sift.SiftProcessor@714f91da - End of configuration.
[testng] [2024-10-08 08:49:31,508] [pool-1-thread-3] Initializing /data/johannes/template.labels:
[testng] 08:49:31,508 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 08:49:31,508 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:49:31,509 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-08_08-49-31.log]
[testng] 08:49:31,509 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68084013 - End of configuration.
[testng] [2024-10-08 08:49:31,946] [pool-1-thread-2] Initializing /data/public/ignacio/test.am:
[testng] 08:49:31,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 08:49:31,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:49:31,946 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-08_08-49-31.log]
[testng] 08:49:31,947 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a91343e - End of configuration.
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 636, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 29 seconds
Finished: SUCCESS