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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