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Started by upstream project "BIOFORMATS-test-repo" build number 31 originally caused by: Started by upstream project "Trigger" build number 35 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins11553247714275096363.sh + '[' amira = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_4096_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 test-automated: [testng] File leak detector installed [testng] 07:13:33,549 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 07:13:33,551 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 07:13:33,551 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 07:13:33,552 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 07:13:33,552 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 07:13:33,553 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 07:13:33,553 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 07:13:33,553 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 07:13:33,554 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 07:13:33,554 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 07:13:33,554 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 07:13:33,554 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 07:13:33,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 07:13:33,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 07:13:33,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 07:13:33,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 07:13:33,904 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 07:13:33,904 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 07:13:33,904 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 07:13:33,905 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 07:13:33,905 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 07:13:33,911 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 07:13:33,911 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 357 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-12 07:13:33,925] [main] java.version = 1.8.0_342 [testng] 07:13:33,930 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 07:13:33,930 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:13:34,007 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-12_07-13-33.log] [testng] 07:13:34,009 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-04-12 07:13:34,012] [main] testng.directory = /data [testng] [2024-04-12 07:13:34,013] [main] testng.configDirectory = /config [testng] [2024-04-12 07:13:34,031] [main] testng.multiplier = 1.0 [testng] [2024-04-12 07:13:34,032] [main] testng.in-memory = false [testng] [2024-04-12 07:13:34,032] [main] testng.allow-missing = false [testng] [2024-04-12 07:13:34,032] [main] user.language = en [testng] [2024-04-12 07:13:34,032] [main] user.country = ${user.country} [testng] [2024-04-12 07:13:34,032] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-04-12 07:13:34,667] [main] ---------------------------------------- [testng] [2024-04-12 07:13:34,667] [main] Total files: 15 [testng] [2024-04-12 07:13:34,667] [main] Scan time: 0.635 s (42 ms/file) [testng] [2024-04-12 07:13:34,667] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 12 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-12 07:13:36,093] [pool-1-thread-1] Initializing /data/samples/emptykey/test.am: [testng] 07:13:36,093 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 07:13:36,093 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:13:36,095 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-12_07-13-36.log] [testng] 07:13:36,095 |-INFO in ch.qos.logback.core.sift.SiftProcessor@92858b9 - End of configuration. [testng] [2024-04-12 07:13:36,122] [pool-1-thread-12] Initializing /data/public/ignacio/test.am: [testng] 07:13:36,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 07:13:36,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:13:36,123 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-12_07-13-36.log] [testng] 07:13:36,124 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69dc4276 - End of configuration. [testng] [2024-04-12 07:13:36,136] [pool-1-thread-11] Initializing /data/jeremy/Virus_Membrane7-screenshot.PNG: [testng] 07:13:36,137 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 07:13:36,137 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:13:36,138 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-12_07-13-36.log] [testng] 07:13:36,138 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78ab7667 - End of configuration. [testng] [2024-04-12 07:13:36,143] [pool-1-thread-10] Initializing /data/public/imagesc-50585/BF_CheckMIB.am: [testng] 07:13:36,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 07:13:36,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:13:36,144 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-12_07-13-36.log] [testng] 07:13:36,145 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66f81351 - End of configuration. [testng] [2024-04-12 07:13:36,157] [pool-1-thread-9] Initializing /data/jcb/201108088/Haberman-Fig4A-original.am: [testng] 07:13:36,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 07:13:36,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:13:36,158 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-12_07-13-36.log] [testng] 07:13:36,159 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1503ea31 - End of configuration. [testng] [2024-04-12 07:13:36,186] [pool-1-thread-8] Initializing /data/johannes/template.labels: [testng] 07:13:36,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 07:13:36,187 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:13:36,188 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-12_07-13-36.log] [testng] 07:13:36,189 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b4e75fc - End of configuration. [testng] [2024-04-12 07:13:36,206] [pool-1-thread-7] Initializing /data/johannes/template.grey: [testng] 07:13:36,206 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 07:13:36,207 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:13:36,208 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-12_07-13-36.log] [testng] 07:13:36,209 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13080500 - End of configuration. [testng] [2024-04-12 07:13:36,263] [pool-1-thread-6] Initializing /data/public/imagesc-50585/BF_Check.tif: [testng] 07:13:36,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 07:13:36,264 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:13:36,264 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-12_07-13-36.log] [testng] 07:13:36,265 |-INFO in ch.qos.logback.core.sift.SiftProcessor@278bc19 - End of configuration. [testng] [2024-04-12 07:13:36,289] [pool-1-thread-5] Initializing /data/jeremy/Virus_Membrane7.am: [testng] 07:13:36,289 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 07:13:36,289 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:13:36,290 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-12_07-13-36.log] [testng] 07:13:36,291 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d5f595e - End of configuration. [testng] [2024-04-12 07:13:36,317] [pool-1-thread-4] Initializing /data/public/imagesc-50585/BF_CheckAmira.am: [testng] 07:13:36,317 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 07:13:36,317 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:13:36,318 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-12_07-13-36.log] [testng] 07:13:36,319 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f41ada2 - End of configuration. [testng] [2024-04-12 07:13:36,331] [pool-1-thread-3] Initializing /data/jeremy/Hiv_spikes.am: [testng] 07:13:36,331 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 07:13:36,331 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:13:36,332 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-12_07-13-36.log] [testng] 07:13:36,332 |-INFO in ch.qos.logback.core.sift.SiftProcessor@854dc10 - End of configuration. [testng] [2024-04-12 07:13:36,350] [pool-1-thread-2] Initializing /data/ilya/test.am: [testng] 07:13:36,350 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 07:13:36,350 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:13:36,351 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-12_07-13-36.log] [testng] 07:13:36,351 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62af8dcb - 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