Started by upstream project "BIOFORMATS-test-repo" build number 295
originally caused by:
Started by upstream project "Trigger" build number 314
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7
[BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins9974649395478663721.sh
+ '[' amira = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_46596_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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release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] 00:30:06,236 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 00:30:06,237 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service.
[testng] 00:30:06,237 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:30:06,238 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 00:30:06,238 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 00:30:06,239 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 00:30:06,239 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 00:30:06,239 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:30:06,239 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 00:30:06,240 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 00:30:06,240 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 00:30:06,241 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 00:30:06,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 00:30:06,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 00:30:06,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 00:30:06,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 00:30:06,433 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 00:30:06,433 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 00:30:06,433 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 00:30:06,433 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 00:30:06,434 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration.
[testng] 00:30:06,434 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point
[testng] 00:30:06,434 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 195 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-12-19 00:30:06,443] [main] java.version = 21
[testng] 00:30:06,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 00:30:06,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:30:06,488 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-19_00-30-06.log]
[testng] 00:30:06,490 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration.
[testng] [2024-12-19 00:30:06,491] [main] testng.directory = /data
[testng] [2024-12-19 00:30:06,492] [main] testng.configDirectory = /config
[testng] [2024-12-19 00:30:06,501] [main] testng.multiplier = 1.0
[testng] [2024-12-19 00:30:06,501] [main] testng.in-memory = false
[testng] [2024-12-19 00:30:06,501] [main] testng.allow-missing = false
[testng] [2024-12-19 00:30:06,501] [main] user.language = en
[testng] [2024-12-19 00:30:06,501] [main] user.country = ${user.country}
[testng] [2024-12-19 00:30:06,501] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-12-19 00:30:11,579] [main] ----------------------------------------
[testng] [2024-12-19 00:30:11,580] [main] Total files: 15
[testng] [2024-12-19 00:30:11,580] [main] Scan time: 5.078 s (338 ms/file)
[testng] [2024-12-19 00:30:11,580] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 12 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-12-19 00:30:22,299] [pool-1-thread-1] Initializing /data/jeremy/Virus_Membrane7.am:
[testng] 00:30:22,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 00:30:22,300 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:30:22,301 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-19_00-30-22.log]
[testng] 00:30:22,301 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d82704a - End of configuration.
[testng] [2024-12-19 00:30:22,715] [pool-1-thread-12] Initializing /data/samples/emptykey/test.am:
[testng] 00:30:22,715 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 00:30:22,715 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:30:22,716 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-19_00-30-22.log]
[testng] 00:30:22,716 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ca6ae30 - End of configuration.
[testng] [2024-12-19 00:30:23,118] [pool-1-thread-11] Initializing /data/public/ignacio/test.am:
[testng] 00:30:23,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 00:30:23,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:30:23,119 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-19_00-30-23.log]
[testng] 00:30:23,119 |-INFO in ch.qos.logback.core.sift.SiftProcessor@cbfe87d - End of configuration.
[testng] [2024-12-19 00:30:23,535] [pool-1-thread-10] Initializing /data/johannes/template.grey:
[testng] 00:30:23,536 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 00:30:23,536 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:30:23,536 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-19_00-30-23.log]
[testng] 00:30:23,537 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5df9bae7 - End of configuration.
[testng] [2024-12-19 00:30:23,946] [pool-1-thread-9] Initializing /data/jeremy/Hiv_spikes.am:
[testng] 00:30:23,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 00:30:23,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:30:23,947 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-19_00-30-23.log]
[testng] 00:30:23,947 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a381df0 - End of configuration.
[testng] [2024-12-19 00:30:24,380] [pool-1-thread-8] Initializing /data/ilya/test.am:
[testng] 00:30:24,380 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 00:30:24,380 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:30:24,380 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-19_00-30-24.log]
[testng] 00:30:24,381 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43d182e2 - End of configuration.
[testng] [2024-12-19 00:30:24,826] [pool-1-thread-7] Initializing /data/public/imagesc-50585/BF_CheckAmira.am:
[testng] 00:30:24,826 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 00:30:24,826 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:30:24,827 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-19_00-30-24.log]
[testng] 00:30:24,827 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53da0100 - End of configuration.
[testng] [2024-12-19 00:30:25,322] [pool-1-thread-6] Initializing /data/public/imagesc-50585/BF_Check.tif:
[testng] 00:30:25,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 00:30:25,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:30:25,323 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-19_00-30-25.log]
[testng] 00:30:25,324 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2db44267 - End of configuration.
[testng] [2024-12-19 00:30:26,345] [pool-1-thread-5] Initializing /data/jeremy/Virus_Membrane7-screenshot.PNG:
[testng] 00:30:26,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 00:30:26,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:30:26,346 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-19_00-30-26.log]
[testng] 00:30:26,346 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11028e96 - End of configuration.
[testng] [2024-12-19 00:30:26,380] [pool-1-thread-4] Initializing /data/johannes/template.labels:
[testng] 00:30:26,380 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 00:30:26,380 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:30:26,381 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-19_00-30-26.log]
[testng] 00:30:26,381 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3696316c - End of configuration.
[testng] [2024-12-19 00:30:26,755] [pool-1-thread-3] Initializing /data/public/imagesc-50585/BF_CheckMIB.am:
[testng] 00:30:26,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 00:30:26,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:30:26,756 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-19_00-30-26.log]
[testng] 00:30:26,757 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f484c66 - End of configuration.
[testng] [2024-12-19 00:30:27,194] [pool-1-thread-2] Initializing /data/jcb/201108088/Haberman-Fig4A-original.am:
[testng] 00:30:27,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 00:30:27,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 00:30:27,195 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-19_00-30-27.log]
[testng] 00:30:27,196 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5172df74 - 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: 31 seconds
Finished: SUCCESS