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Started by upstream project "BIOFORMATS-test-repo" build number 263 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins5467299093428606526.sh + '[' amira = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_41472_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 15:33:25,764 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 15:33:25,765 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 15:33:25,765 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 15:33:25,766 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 15:33:25,767 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 15:33:25,767 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 15:33:25,767 |-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] 15:33:25,767 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 15:33:25,768 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 15:33:25,769 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 15:33:25,769 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 15:33:25,769 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 15:33:25,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 15:33:25,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 15:33:25,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 15:33:25,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 15:33:25,969 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 15:33:25,970 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 15:33:25,970 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 15:33:25,970 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 15:33:25,970 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 15:33:25,971 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 15:33:25,971 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 203 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-21 15:33:25,980] [main] java.version = 21 [testng] 15:33:25,983 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 15:33:25,983 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:33:26,023 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-21_15-33-25.log] [testng] 15:33:26,025 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-11-21 15:33:26,026] [main] testng.directory = /data [testng] [2024-11-21 15:33:26,027] [main] testng.configDirectory = /config [testng] [2024-11-21 15:33:26,035] [main] testng.multiplier = 1.0 [testng] [2024-11-21 15:33:26,036] [main] testng.in-memory = false [testng] [2024-11-21 15:33:26,036] [main] testng.allow-missing = false [testng] [2024-11-21 15:33:26,036] [main] user.language = en [testng] [2024-11-21 15:33:26,036] [main] user.country = ${user.country} [testng] [2024-11-21 15:33:26,036] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-21 15:33:31,455] [main] ---------------------------------------- [testng] [2024-11-21 15:33:31,455] [main] Total files: 15 [testng] [2024-11-21 15:33:31,455] [main] Scan time: 5.419 s (361 ms/file) [testng] [2024-11-21 15:33:31,456] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 12 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-21 15:33:44,227] [pool-1-thread-1] Initializing /data/jcb/201108088/Haberman-Fig4A-original.am: [testng] 15:33:44,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 15:33:44,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:33:44,229 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-21_15-33-44.log] [testng] 15:33:44,230 |-INFO in ch.qos.logback.core.sift.SiftProcessor@365154b8 - End of configuration. [testng] [2024-11-21 15:33:45,659] [pool-1-thread-12] Initializing /data/public/imagesc-50585/BF_CheckMIB.am: [testng] 15:33:45,660 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 15:33:45,660 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:33:45,661 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-21_15-33-45.log] [testng] 15:33:45,661 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52e94a03 - End of configuration. [testng] [2024-11-21 15:33:46,610] [pool-1-thread-11] Initializing /data/jeremy/Hiv_spikes.am: [testng] 15:33:46,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 15:33:46,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:33:46,611 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-21_15-33-46.log] [testng] 15:33:46,612 |-INFO in ch.qos.logback.core.sift.SiftProcessor@629fa43d - End of configuration. [testng] [2024-11-21 15:33:47,570] [pool-1-thread-10] Initializing /data/public/imagesc-50585/BF_Check.tif: [testng] 15:33:47,570 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 15:33:47,570 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:33:47,571 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-21_15-33-47.log] [testng] 15:33:47,571 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a10c7ca - End of configuration. [testng] [2024-11-21 15:33:50,010] [pool-1-thread-9] Initializing /data/johannes/template.grey: [testng] 15:33:50,010 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 15:33:50,010 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:33:50,011 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-21_15-33-50.log] [testng] 15:33:50,011 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5bd4979a - End of configuration. [testng] [2024-11-21 15:33:50,990] [pool-1-thread-8] Initializing /data/jeremy/Virus_Membrane7-screenshot.PNG: [testng] 15:33:50,990 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 15:33:50,990 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:33:50,991 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-21_15-33-50.log] [testng] 15:33:50,991 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ea0c1f0 - End of configuration. [testng] [2024-11-21 15:33:51,061] [pool-1-thread-7] Initializing /data/ilya/test.am: [testng] 15:33:51,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 15:33:51,062 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:33:51,062 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-21_15-33-51.log] [testng] 15:33:51,063 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b9e0b8a - End of configuration. [testng] [2024-11-21 15:33:52,046] [pool-1-thread-6] Initializing /data/samples/emptykey/test.am: [testng] 15:33:52,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 15:33:52,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:33:52,047 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-21_15-33-52.log] [testng] 15:33:52,047 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63e0483 - End of configuration. [testng] [2024-11-21 15:33:53,065] [pool-1-thread-5] Initializing /data/johannes/template.labels: [testng] 15:33:53,066 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 15:33:53,066 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:33:53,066 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-21_15-33-53.log] [testng] 15:33:53,067 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6522fb08 - End of configuration. [testng] [2024-11-21 15:33:54,023] [pool-1-thread-4] Initializing /data/public/imagesc-50585/BF_CheckAmira.am: [testng] 15:33:54,024 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 15:33:54,024 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:33:54,024 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-21_15-33-54.log] [testng] 15:33:54,025 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b529531 - End of configuration. [testng] [2024-11-21 15:33:54,751] [pool-1-thread-3] Initializing /data/jeremy/Virus_Membrane7.am: [testng] 15:33:54,751 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 15:33:54,751 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:33:54,752 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-21_15-33-54.log] [testng] 15:33:54,752 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d6b7360 - End of configuration. [testng] [2024-11-21 15:33:55,309] [pool-1-thread-2] Initializing /data/public/ignacio/test.am: [testng] 15:33:55,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 15:33:55,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:33:55,310 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-21_15-33-55.log] [testng] 15:33:55,310 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e1e360c - 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: 41 seconds Finished: SUCCESS