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Started by upstream project "BIOFORMATS-test-repo" build number 71 originally caused by: Started by upstream project "Trigger" build number 79 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/jenkins4347677789001314303.sh + '[' amira = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_10657_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] 03:52:46,268 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:52:46,270 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 03:52:46,270 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:52:46,271 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:52:46,271 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:52:46,272 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:52:46,272 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 03:52:46,272 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:52:46,272 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:52:46,273 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:52:46,273 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:52:46,274 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:52:46,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:52:46,460 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:52:46,482 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:52:46,483 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:52:46,489 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:52:46,489 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:52:46,489 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:52:46,490 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:52:46,490 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 03:52:46,491 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 03:52:46,492 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 219 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-22 03:52:46,501] [main] java.version = 17.0.2 [testng] 03:52:46,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:52:46,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:52:46,551 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-22_03-52-46.log] [testng] 03:52:46,552 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-05-22 03:52:46,554] [main] testng.directory = /data [testng] [2024-05-22 03:52:46,554] [main] testng.configDirectory = /config [testng] [2024-05-22 03:52:46,564] [main] testng.multiplier = 1.0 [testng] [2024-05-22 03:52:46,565] [main] testng.in-memory = false [testng] [2024-05-22 03:52:46,565] [main] testng.allow-missing = false [testng] [2024-05-22 03:52:46,565] [main] user.language = en [testng] [2024-05-22 03:52:46,565] [main] user.country = ${user.country} [testng] [2024-05-22 03:52:46,566] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-05-22 03:52:47,209] [main] ---------------------------------------- [testng] [2024-05-22 03:52:47,209] [main] Total files: 15 [testng] [2024-05-22 03:52:47,209] [main] Scan time: 0.643 s (42 ms/file) [testng] [2024-05-22 03:52:47,209] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 12 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-22 03:52:48,259] [pool-1-thread-1] Initializing /data/johannes/template.labels: [testng] 03:52:48,259 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:52:48,260 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:52:48,261 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-22_03-52-48.log] [testng] 03:52:48,262 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b9b656e - End of configuration. [testng] [2024-05-22 03:52:48,294] [pool-1-thread-12] Initializing /data/jeremy/Virus_Membrane7.am: [testng] 03:52:48,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:52:48,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:52:48,296 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-22_03-52-48.log] [testng] 03:52:48,297 |-INFO in ch.qos.logback.core.sift.SiftProcessor@352d1dab - End of configuration. [testng] [2024-05-22 03:52:48,332] [pool-1-thread-11] Initializing /data/public/ignacio/test.am: [testng] 03:52:48,332 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:52:48,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:52:48,333 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-22_03-52-48.log] [testng] 03:52:48,334 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ee20634 - End of configuration. [testng] [2024-05-22 03:52:48,349] [pool-1-thread-10] Initializing /data/public/imagesc-50585/BF_CheckAmira.am: [testng] 03:52:48,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:52:48,350 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:52:48,350 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-22_03-52-48.log] [testng] 03:52:48,351 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30a776f0 - End of configuration. [testng] [2024-05-22 03:52:48,366] [pool-1-thread-9] Initializing /data/jeremy/Hiv_spikes.am: [testng] 03:52:48,367 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:52:48,367 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:52:48,368 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-22_03-52-48.log] [testng] 03:52:48,368 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e213dfd - End of configuration. [testng] [2024-05-22 03:52:48,389] [pool-1-thread-8] Initializing /data/samples/emptykey/test.am: [testng] 03:52:48,389 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:52:48,389 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:52:48,390 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-22_03-52-48.log] [testng] 03:52:48,391 |-INFO in ch.qos.logback.core.sift.SiftProcessor@310f2c99 - End of configuration. [testng] [2024-05-22 03:52:48,407] [pool-1-thread-7] Initializing /data/jcb/201108088/Haberman-Fig4A-original.am: [testng] 03:52:48,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:52:48,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:52:48,409 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-22_03-52-48.log] [testng] 03:52:48,409 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f8c89ad - End of configuration. [testng] [2024-05-22 03:52:48,449] [pool-1-thread-6] Initializing /data/jeremy/Virus_Membrane7-screenshot.PNG: [testng] 03:52:48,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:52:48,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:52:48,450 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-22_03-52-48.log] [testng] 03:52:48,450 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33b4dd5e - End of configuration. [testng] [2024-05-22 03:52:48,463] [pool-1-thread-5] Initializing /data/public/imagesc-50585/BF_CheckMIB.am: [testng] 03:52:48,464 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:52:48,464 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:52:48,465 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-22_03-52-48.log] [testng] 03:52:48,465 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22616914 - End of configuration. [testng] [2024-05-22 03:52:48,485] [pool-1-thread-4] Initializing /data/ilya/test.am: [testng] 03:52:48,485 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:52:48,485 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:52:48,486 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-22_03-52-48.log] [testng] 03:52:48,486 |-INFO in ch.qos.logback.core.sift.SiftProcessor@84029e7 - End of configuration. [testng] [2024-05-22 03:52:48,537] [pool-1-thread-3] Initializing /data/public/imagesc-50585/BF_Check.tif: [testng] 03:52:48,537 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:52:48,537 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:52:48,538 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-22_03-52-48.log] [testng] 03:52:48,539 |-INFO in ch.qos.logback.core.sift.SiftProcessor@401acfa7 - End of configuration. [testng] [2024-05-22 03:52:48,592] [pool-1-thread-2] Initializing /data/johannes/template.grey: [testng] 03:52:48,592 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:52:48,592 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:52:48,593 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-22_03-52-48.log] [testng] 03:52:48,594 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b26cddb - 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: 10 seconds Finished: SUCCESS