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Started by upstream project "BIOFORMATS-test-repo" build number 388 originally caused by: Started by upstream project "Trigger" build number 411 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@11 [BIOFORMATS-test-folder@11] $ /bin/bash -xe /tmp/jenkins6330117187172041046.sh + '[' amira = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_61346_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] 00:23:57,082 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:23:57,083 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service. [testng] 00:23:57,083 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:23:57,084 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:23:57,085 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:23:57,085 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:23:57,085 |-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] 00:23:57,085 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:23:57,086 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:23:57,086 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:23:57,087 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:23:57,087 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:23:57,262 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:23:57,262 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:23:57,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:23:57,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:23:57,294 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:23:57,294 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:23:57,294 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:23:57,295 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:23:57,295 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration. [testng] 00:23:57,296 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point [testng] 00:23:57,296 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 210 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-23 00:23:57,308] [main] java.version = 17.0.2 [testng] 00:23:57,313 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:23:57,313 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:23:57,356 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-23_00-23-57.log] [testng] 00:23:57,357 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration. [testng] [2025-03-23 00:23:57,359] [main] testng.directory = /data [testng] [2025-03-23 00:23:57,360] [main] testng.configDirectory = /config [testng] [2025-03-23 00:23:57,369] [main] testng.multiplier = 1.0 [testng] [2025-03-23 00:23:57,370] [main] testng.in-memory = false [testng] [2025-03-23 00:23:57,370] [main] testng.allow-missing = false [testng] [2025-03-23 00:23:57,370] [main] user.language = en [testng] [2025-03-23 00:23:57,371] [main] user.country = ${user.country} [testng] [2025-03-23 00:23:57,371] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-23 00:24:08,003] [main] ---------------------------------------- [testng] [2025-03-23 00:24:08,003] [main] Total files: 15 [testng] [2025-03-23 00:24:08,003] [main] Scan time: 10.632 s (708 ms/file) [testng] [2025-03-23 00:24:08,003] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 12 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-23 00:24:38,773] [pool-1-thread-1] Initializing /data/jeremy/Virus_Membrane7-screenshot.PNG: [testng] 00:24:38,774 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:24:38,774 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:38,775 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-23_00-24-38.log] [testng] 00:24:38,776 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1fb29689 - End of configuration. [testng] [2025-03-23 00:24:38,909] [pool-1-thread-12] Initializing /data/jcb/201108088/Haberman-Fig4A-original.am: [testng] 00:24:38,909 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:24:38,910 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:38,910 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-23_00-24-38.log] [testng] 00:24:38,911 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7901443d - End of configuration. [testng] [2025-03-23 00:24:40,529] [pool-1-thread-11] Initializing /data/public/imagesc-50585/BF_CheckAmira.am: [testng] 00:24:40,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:24:40,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:40,530 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-23_00-24-40.log] [testng] 00:24:40,531 |-INFO in ch.qos.logback.core.sift.SiftProcessor@604c69e - End of configuration. [testng] [2025-03-23 00:24:42,098] [pool-1-thread-10] Initializing /data/jeremy/Virus_Membrane7.am: [testng] 00:24:42,098 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:24:42,098 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:42,099 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-23_00-24-42.log] [testng] 00:24:42,100 |-INFO in ch.qos.logback.core.sift.SiftProcessor@227cee7b - End of configuration. [testng] [2025-03-23 00:24:43,582] [pool-1-thread-9] Initializing /data/johannes/template.labels: [testng] 00:24:43,582 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:24:43,582 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:43,583 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-23_00-24-43.log] [testng] 00:24:43,584 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75615228 - End of configuration. [testng] [2025-03-23 00:24:45,130] [pool-1-thread-8] Initializing /data/public/imagesc-50585/BF_CheckMIB.am: [testng] 00:24:45,130 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:24:45,131 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:45,131 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-23_00-24-45.log] [testng] 00:24:45,132 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63cda7e6 - End of configuration. [testng] [2025-03-23 00:24:46,568] [pool-1-thread-7] Initializing /data/public/imagesc-50585/BF_Check.tif: [testng] 00:24:46,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:24:46,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:46,569 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-23_00-24-46.log] [testng] 00:24:46,569 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5394169b - End of configuration. [testng] [2025-03-23 00:24:50,220] [pool-1-thread-6] Initializing /data/ilya/test.am: [testng] 00:24:50,220 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:24:50,220 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:50,221 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-23_00-24-50.log] [testng] 00:24:50,221 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3100407b - End of configuration. [testng] [2025-03-23 00:24:51,346] [pool-1-thread-5] Initializing /data/public/ignacio/test.am: [testng] 00:24:51,346 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:24:51,346 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:51,347 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-23_00-24-51.log] [testng] 00:24:51,347 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6971659a - End of configuration. [testng] [2025-03-23 00:24:52,741] [pool-1-thread-4] Initializing /data/johannes/template.grey: [testng] 00:24:52,742 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:24:52,742 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:52,742 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-23_00-24-52.log] [testng] 00:24:52,743 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ccd0ddd - End of configuration. [testng] [2025-03-23 00:24:54,115] [pool-1-thread-3] Initializing /data/samples/emptykey/test.am: [testng] 00:24:54,115 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:24:54,115 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:54,116 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-23_00-24-54.log] [testng] 00:24:54,116 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8f068e2 - End of configuration. [testng] [2025-03-23 00:24:55,544] [pool-1-thread-2] Initializing /data/jeremy/Hiv_spikes.am: [testng] 00:24:55,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:24:55,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:24:55,545 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-23_00-24-55.log] [testng] 00:24:55,546 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3fee6804 - 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: 1 minute 22 seconds Finished: SUCCESS