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Started by upstream project "BIOFORMATS-test-repo" build number 386 originally caused by: Started by upstream project "Trigger" build number 408 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@14 [BIOFORMATS-test-folder@14] $ /bin/bash -xe /tmp/jenkins2238150073916889154.sh + '[' amira = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_61016_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 22:22:37,001 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 22:22:37,002 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - No custom configurators were discovered as a service. [testng] 22:22:37,002 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 22:22:37,003 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 22:22:37,004 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 22:22:37,004 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 22:22:37,005 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 22:22:37,005 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 22:22:37,005 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 22:22:37,006 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 22:22:37,006 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 22:22:37,006 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 22:22:37,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 22:22:37,174 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 22:22:37,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 22:22:37,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 22:22:37,207 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 22:22:37,207 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 22:22:37,207 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 22:22:37,208 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 22:22:37,208 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@4310d43 - End of configuration. [testng] 22:22:37,209 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@1b11171f - Registering current configuration as safe fallback point [testng] 22:22:37,209 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 204 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-20 22:22:37,218] [main] java.version = 21 [testng] 22:22:37,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 22:22:37,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 22:22:37,264 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-20_22-22-37.log] [testng] 22:22:37,266 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69504ae9 - End of configuration. [testng] [2025-03-20 22:22:37,267] [main] testng.directory = /data [testng] [2025-03-20 22:22:37,267] [main] testng.configDirectory = /config [testng] [2025-03-20 22:22:37,276] [main] testng.multiplier = 1.0 [testng] [2025-03-20 22:22:37,277] [main] testng.in-memory = false [testng] [2025-03-20 22:22:37,277] [main] testng.allow-missing = false [testng] [2025-03-20 22:22:37,277] [main] user.language = en [testng] [2025-03-20 22:22:37,277] [main] user.country = ${user.country} [testng] [2025-03-20 22:22:37,277] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-20 22:22:47,153] [main] ---------------------------------------- [testng] [2025-03-20 22:22:47,153] [main] Total files: 15 [testng] [2025-03-20 22:22:47,154] [main] Scan time: 9.876 s (658 ms/file) [testng] [2025-03-20 22:22:47,154] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 12 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-20 22:23:11,230] [pool-1-thread-1] Initializing /data/public/imagesc-50585/BF_CheckMIB.am: [testng] 22:23:11,231 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 22:23:11,231 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 22:23:11,233 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-20_22-23-11.log] [testng] 22:23:11,233 |-INFO in ch.qos.logback.core.sift.SiftProcessor@791a7449 - End of configuration. [testng] [2025-03-20 22:23:12,309] [pool-1-thread-12] Initializing /data/public/imagesc-50585/BF_CheckAmira.am: [testng] 22:23:12,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 22:23:12,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 22:23:12,310 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-20_22-23-12.log] [testng] 22:23:12,310 |-INFO in ch.qos.logback.core.sift.SiftProcessor@630b8c0a - End of configuration. [testng] [2025-03-20 22:23:13,216] [pool-1-thread-11] Initializing /data/johannes/template.labels: [testng] 22:23:13,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 22:23:13,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 22:23:13,218 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-20_22-23-13.log] [testng] 22:23:13,218 |-INFO in ch.qos.logback.core.sift.SiftProcessor@193ac080 - End of configuration. [testng] [2025-03-20 22:23:14,223] [pool-1-thread-10] Initializing /data/jeremy/Hiv_spikes.am: [testng] 22:23:14,224 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 22:23:14,224 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 22:23:14,224 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-20_22-23-14.log] [testng] 22:23:14,225 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b31582d - End of configuration. [testng] [2025-03-20 22:23:15,082] [pool-1-thread-9] Initializing /data/ilya/test.am: [testng] 22:23:15,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 22:23:15,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 22:23:15,084 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-20_22-23-15.log] [testng] 22:23:15,085 |-INFO in ch.qos.logback.core.sift.SiftProcessor@461603bd - End of configuration. [testng] [2025-03-20 22:23:15,988] [pool-1-thread-8] Initializing /data/public/ignacio/test.am: [testng] 22:23:15,988 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 22:23:15,988 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 22:23:15,989 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-20_22-23-15.log] [testng] 22:23:15,989 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f1ad6e4 - End of configuration. [testng] [2025-03-20 22:23:16,822] [pool-1-thread-7] Initializing /data/public/imagesc-50585/BF_Check.tif: [testng] 22:23:16,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 22:23:16,823 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 22:23:16,823 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-20_22-23-16.log] [testng] 22:23:16,824 |-INFO in ch.qos.logback.core.sift.SiftProcessor@260903aa - End of configuration. [testng] [2025-03-20 22:23:18,967] [pool-1-thread-6] Initializing /data/jeremy/Virus_Membrane7.am: [testng] 22:23:18,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 22:23:18,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 22:23:18,969 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-20_22-23-18.log] [testng] 22:23:18,969 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fb216bc - End of configuration. [testng] [2025-03-20 22:23:19,788] [pool-1-thread-5] Initializing /data/jeremy/Virus_Membrane7-screenshot.PNG: [testng] 22:23:19,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 22:23:19,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 22:23:19,789 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-20_22-23-19.log] [testng] 22:23:19,789 |-INFO in ch.qos.logback.core.sift.SiftProcessor@629fa43d - End of configuration. [testng] [2025-03-20 22:23:19,852] [pool-1-thread-4] Initializing /data/jcb/201108088/Haberman-Fig4A-original.am: [testng] 22:23:19,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 22:23:19,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 22:23:19,853 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-20_22-23-19.log] [testng] 22:23:19,854 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a10c7ca - End of configuration. [testng] [2025-03-20 22:23:21,015] [pool-1-thread-3] Initializing /data/samples/emptykey/test.am: [testng] 22:23:21,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 22:23:21,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 22:23:21,016 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-20_22-23-21.log] [testng] 22:23:21,016 |-INFO in ch.qos.logback.core.sift.SiftProcessor@148c9c87 - End of configuration. [testng] [2025-03-20 22:23:22,203] [pool-1-thread-2] Initializing /data/johannes/template.grey: [testng] 22:23:22,203 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 22:23:22,203 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 22:23:22,204 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-20_22-23-22.log] [testng] 22:23:22,204 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27c23bfe - 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 7 seconds Finished: SUCCESS