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Started by upstream project "BIOFORMATS-test-repo" build number 384 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/jenkins7792431400922107984.sh + '[' amira = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_60706_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] 12:05:53,263 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 12:05:53,264 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service. [testng] 12:05:53,264 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:05:53,265 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:05:53,266 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 12:05:53,266 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 12:05:53,266 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 12:05:53,266 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:05:53,267 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:05:53,267 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 12:05:53,267 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 12:05:53,268 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 12:05:53,423 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 12:05:53,423 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 12:05:53,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 12:05:53,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 12:05:53,450 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 12:05:53,451 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 12:05:53,451 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 12:05:53,451 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 12:05:53,451 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration. [testng] 12:05:53,452 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point [testng] 12:05:53,452 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 185 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-19 12:05:53,461] [main] java.version = 17.0.2 [testng] 12:05:53,464 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 12:05:53,464 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:05:53,504 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-19_12-05-53.log] [testng] 12:05:53,505 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration. [testng] [2025-03-19 12:05:53,507] [main] testng.directory = /data [testng] [2025-03-19 12:05:53,508] [main] testng.configDirectory = /config [testng] [2025-03-19 12:05:53,516] [main] testng.multiplier = 1.0 [testng] [2025-03-19 12:05:53,517] [main] testng.in-memory = false [testng] [2025-03-19 12:05:53,517] [main] testng.allow-missing = false [testng] [2025-03-19 12:05:53,517] [main] user.language = en [testng] [2025-03-19 12:05:53,517] [main] user.country = ${user.country} [testng] [2025-03-19 12:05:53,518] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-19 12:06:00,870] [main] ---------------------------------------- [testng] [2025-03-19 12:06:00,870] [main] Total files: 15 [testng] [2025-03-19 12:06:00,870] [main] Scan time: 7.352 s (490 ms/file) [testng] [2025-03-19 12:06:00,870] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 12 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-19 12:06:14,979] [pool-1-thread-1] Initializing /data/jeremy/Virus_Membrane7-screenshot.PNG: [testng] 12:06:14,980 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 12:06:14,980 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:06:14,982 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-19_12-06-14.log] [testng] 12:06:14,982 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71e3f7c1 - End of configuration. [testng] [2025-03-19 12:06:15,041] [pool-1-thread-12] Initializing /data/jcb/201108088/Haberman-Fig4A-original.am: [testng] 12:06:15,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 12:06:15,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:06:15,042 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-19_12-06-15.log] [testng] 12:06:15,043 |-INFO in ch.qos.logback.core.sift.SiftProcessor@547481cb - End of configuration. [testng] [2025-03-19 12:06:15,562] [pool-1-thread-11] Initializing /data/public/imagesc-50585/BF_CheckAmira.am: [testng] 12:06:15,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 12:06:15,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:06:15,564 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-19_12-06-15.log] [testng] 12:06:15,564 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7211b1de - End of configuration. [testng] [2025-03-19 12:06:16,152] [pool-1-thread-10] Initializing /data/jeremy/Virus_Membrane7.am: [testng] 12:06:16,152 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 12:06:16,152 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:06:16,153 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-19_12-06-16.log] [testng] 12:06:16,153 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75615228 - End of configuration. [testng] [2025-03-19 12:06:16,799] [pool-1-thread-9] Initializing /data/johannes/template.labels: [testng] 12:06:16,799 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 12:06:16,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:06:16,800 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-19_12-06-16.log] [testng] 12:06:16,801 |-INFO in ch.qos.logback.core.sift.SiftProcessor@bce76b3 - End of configuration. [testng] [2025-03-19 12:06:17,423] [pool-1-thread-8] Initializing /data/public/imagesc-50585/BF_CheckMIB.am: [testng] 12:06:17,423 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 12:06:17,423 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:06:17,424 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-19_12-06-17.log] [testng] 12:06:17,424 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3cbb3301 - End of configuration. [testng] [2025-03-19 12:06:18,042] [pool-1-thread-7] Initializing /data/public/imagesc-50585/BF_Check.tif: [testng] 12:06:18,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 12:06:18,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:06:18,044 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-19_12-06-18.log] [testng] 12:06:18,044 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63cda7e6 - End of configuration. [testng] [2025-03-19 12:06:19,511] [pool-1-thread-6] Initializing /data/ilya/test.am: [testng] 12:06:19,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 12:06:19,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:06:19,512 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-19_12-06-19.log] [testng] 12:06:19,512 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5394169b - End of configuration. [testng] [2025-03-19 12:06:20,051] [pool-1-thread-5] Initializing /data/public/ignacio/test.am: [testng] 12:06:20,051 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 12:06:20,051 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:06:20,052 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-19_12-06-20.log] [testng] 12:06:20,052 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3100407b - End of configuration. [testng] [2025-03-19 12:06:20,688] [pool-1-thread-4] Initializing /data/johannes/template.grey: [testng] 12:06:20,689 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 12:06:20,689 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:06:20,690 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-19_12-06-20.log] [testng] 12:06:20,690 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6971659a - End of configuration. [testng] [2025-03-19 12:06:21,246] [pool-1-thread-3] Initializing /data/samples/emptykey/test.am: [testng] 12:06:21,246 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 12:06:21,246 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:06:21,247 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-19_12-06-21.log] [testng] 12:06:21,247 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ccd0ddd - End of configuration. [testng] [2025-03-19 12:06:21,750] [pool-1-thread-2] Initializing /data/jeremy/Hiv_spikes.am: [testng] 12:06:21,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 12:06:21,750 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:06:21,751 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-19_12-06-21.log] [testng] 12:06:21,751 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8f068e2 - 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: 44 seconds Finished: SUCCESS