Started by upstream project "BIOFORMATS-test-repo" build number 298
originally caused by:
Started by upstream project "Trigger" build number 320
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/jenkins7043786934242226854.sh
+ '[' amira = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_47092_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] 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] 00:29:18,262 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 00:29:18,263 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service.
[testng] 00:29:18,263 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:29:18,264 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:29:18,265 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 00:29:18,265 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 00:29:18,265 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 00:29:18,265 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:29:18,266 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:29:18,266 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 00:29:18,266 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 00:29:18,267 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 00:29:18,420 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 00:29:18,420 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 00:29:18,440 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 00:29:18,440 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 00:29:18,445 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 00:29:18,446 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 00:29:18,446 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 00:29:18,446 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 00:29:18,446 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration.
[testng] 00:29:18,447 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point
[testng] 00:29:18,447 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 181 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-12-25 00:29:18,456] [main] java.version = 17.0.2
[testng] 00:29:18,458 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 00:29:18,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:29:18,497 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-25_00-29-18.log]
[testng] 00:29:18,498 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration.
[testng] [2024-12-25 00:29:18,500] [main] testng.directory = /data
[testng] [2024-12-25 00:29:18,500] [main] testng.configDirectory = /config
[testng] [2024-12-25 00:29:18,508] [main] testng.multiplier = 1.0
[testng] [2024-12-25 00:29:18,509] [main] testng.in-memory = false
[testng] [2024-12-25 00:29:18,509] [main] testng.allow-missing = false
[testng] [2024-12-25 00:29:18,509] [main] user.language = en
[testng] [2024-12-25 00:29:18,509] [main] user.country = ${user.country}
[testng] [2024-12-25 00:29:18,510] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-12-25 00:29:23,803] [main] ----------------------------------------
[testng] [2024-12-25 00:29:23,803] [main] Total files: 15
[testng] [2024-12-25 00:29:23,803] [main] Scan time: 5.293 s (352 ms/file)
[testng] [2024-12-25 00:29:23,803] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 12 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-12-25 00:29:36,108] [pool-1-thread-1] Initializing /data/jeremy/Virus_Membrane7.am:
[testng] 00:29:36,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 00:29:36,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:29:36,109 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-25_00-29-36.log]
[testng] 00:29:36,110 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1908405e - End of configuration.
[testng] [2024-12-25 00:29:36,651] [pool-1-thread-12] Initializing /data/public/imagesc-50585/BF_CheckMIB.am:
[testng] 00:29:36,651 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 00:29:36,651 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:29:36,652 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-25_00-29-36.log]
[testng] 00:29:36,652 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57c821cd - End of configuration.
[testng] [2024-12-25 00:29:37,175] [pool-1-thread-11] Initializing /data/jcb/201108088/Haberman-Fig4A-original.am:
[testng] 00:29:37,176 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 00:29:37,176 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:29:37,177 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-25_00-29-37.log]
[testng] 00:29:37,177 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4fa3eb9b - End of configuration.
[testng] [2024-12-25 00:29:37,771] [pool-1-thread-10] Initializing /data/johannes/template.labels:
[testng] 00:29:37,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 00:29:37,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:29:37,772 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-25_00-29-37.log]
[testng] 00:29:37,772 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21c88b86 - End of configuration.
[testng] [2024-12-25 00:29:38,283] [pool-1-thread-9] Initializing /data/public/imagesc-50585/BF_Check.tif:
[testng] 00:29:38,283 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 00:29:38,283 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:29:38,284 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-25_00-29-38.log]
[testng] 00:29:38,285 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65af82f8 - End of configuration.
[testng] [2024-12-25 00:29:39,551] [pool-1-thread-8] Initializing /data/jeremy/Hiv_spikes.am:
[testng] 00:29:39,551 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 00:29:39,551 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:29:39,551 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-25_00-29-39.log]
[testng] 00:29:39,552 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bbd8a9e - End of configuration.
[testng] [2024-12-25 00:29:40,036] [pool-1-thread-7] Initializing /data/ilya/test.am:
[testng] 00:29:40,036 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 00:29:40,036 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:29:40,037 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-25_00-29-40.log]
[testng] 00:29:40,037 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a87b0b0 - End of configuration.
[testng] [2024-12-25 00:29:40,496] [pool-1-thread-6] Initializing /data/johannes/template.grey:
[testng] 00:29:40,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 00:29:40,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:29:40,497 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-25_00-29-40.log]
[testng] 00:29:40,497 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47b92663 - End of configuration.
[testng] [2024-12-25 00:29:41,079] [pool-1-thread-5] Initializing /data/jeremy/Virus_Membrane7-screenshot.PNG:
[testng] 00:29:41,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 00:29:41,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:29:41,080 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-25_00-29-41.log]
[testng] 00:29:41,080 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10033bd5 - End of configuration.
[testng] [2024-12-25 00:29:41,115] [pool-1-thread-4] Initializing /data/public/imagesc-50585/BF_CheckAmira.am:
[testng] 00:29:41,115 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 00:29:41,115 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:29:41,116 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-25_00-29-41.log]
[testng] 00:29:41,116 |-INFO in ch.qos.logback.core.sift.SiftProcessor@196ae177 - End of configuration.
[testng] [2024-12-25 00:29:41,815] [pool-1-thread-3] Initializing /data/samples/emptykey/test.am:
[testng] 00:29:41,815 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 00:29:41,815 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:29:41,816 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-25_00-29-41.log]
[testng] 00:29:41,816 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58fdbaaf - End of configuration.
[testng] [2024-12-25 00:29:42,281] [pool-1-thread-2] Initializing /data/public/ignacio/test.am:
[testng] 00:29:42,281 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 00:29:42,281 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:29:42,282 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-25_00-29-42.log]
[testng] 00:29:42,282 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44859c38 - 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: 36 seconds
Finished: SUCCESS