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Started by upstream project "BIOFORMATS-test-repo" build number 59 originally caused by: Started by upstream project "Trigger" build number 66 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins17720659160976549102.sh + '[' cellomics = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_8769_merge_ci -v /uod/idr/repos/curated/cellomics:/data -v /uod/idr-scratch/merge-ci/curated/cellomics:/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] 02:14:55,368 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:14:55,372 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 02:14:55,372 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:14:55,374 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:14:55,374 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:14:55,375 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:14:55,375 |-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] 02:14:55,375 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:14:55,376 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:14:55,376 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:14:55,376 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:14:55,377 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:14:55,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:14:55,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:14:55,696 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:14:55,697 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:14:55,708 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:14:55,708 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:14:55,709 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:14:55,709 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:14:55,709 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 02:14:55,710 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 02:14:55,710 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 334 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-10 02:14:55,724] [main] java.version = 1.8.0_342 [testng] 02:14:55,729 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:14:55,729 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:14:55,782 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-10_02-14-55.log] [testng] 02:14:55,784 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-05-10 02:14:55,787] [main] testng.directory = /data [testng] [2024-05-10 02:14:55,787] [main] testng.configDirectory = /config [testng] [2024-05-10 02:14:55,805] [main] testng.multiplier = 1.0 [testng] [2024-05-10 02:14:55,806] [main] testng.in-memory = false [testng] [2024-05-10 02:14:55,806] [main] testng.allow-missing = false [testng] [2024-05-10 02:14:55,806] [main] user.language = en [testng] [2024-05-10 02:14:55,806] [main] user.country = ${user.country} [testng] [2024-05-10 02:14:55,806] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-05-10 02:15:04,833] [main] ---------------------------------------- [testng] [2024-05-10 02:15:04,834] [main] Total files: 2539 [testng] [2024-05-10 02:15:04,834] [main] Scan time: 9.027 s (3 ms/file) [testng] [2024-05-10 02:15:04,834] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-10 02:15:07,536] [pool-1-thread-1] Initializing /data/samples/different-field-count/plate_B03f00d0.C01: [testng] 02:15:07,537 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:15:07,537 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:07,539 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-10_02-15-07.log] [testng] 02:15:07,540 |-INFO in ch.qos.logback.core.sift.SiftProcessor@831f92b - End of configuration. [testng] [2024-05-10 02:15:07,630] [pool-1-thread-12] Initializing /data/omar/FB03f00d0.C01: [testng] 02:15:07,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:15:07,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:07,631 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-10_02-15-07.log] [testng] 02:15:07,632 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7bf106de - End of configuration. [testng] [2024-05-10 02:15:07,663] [pool-1-thread-11] Initializing /data/samples/plate-size/plate_B03f00d0.C01: [testng] 02:15:07,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:15:07,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:07,664 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-10_02-15-07.log] [testng] 02:15:07,665 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7747102f - End of configuration. [testng] [2024-05-10 02:15:07,697] [pool-1-thread-10] Initializing /data/lee/icd002235_090127090001_a01f00d1.c01: [testng] 02:15:07,697 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:15:07,697 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:07,698 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-10_02-15-07.log] [testng] 02:15:07,698 |-INFO in ch.qos.logback.core.sift.SiftProcessor@584a296d - End of configuration. [testng] [2024-05-10 02:15:07,713] [pool-1-thread-9] Initializing /data/johannes/MFGTMP_081128200001_A02f239d1.C01: [testng] 02:15:07,713 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:15:07,713 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:07,714 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-10_02-15-07.log] [testng] 02:15:07,714 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47260f61 - End of configuration. [testng] [2024-05-10 02:15:07,749] [pool-1-thread-8] Initializing /data/qa-7352/test/MFGTMP-PC_130509120002_B02f00d0.C01: [testng] 02:15:07,749 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:15:07,749 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:07,750 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-10_02-15-07.log] [testng] 02:15:07,750 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b0c478 - End of configuration. [testng] [2024-05-10 02:15:07,913] [pool-1-thread-7] Initializing /data/johannes/MFGTMP_081222130005_E07f00d0.C01: [testng] 02:15:07,914 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:15:07,914 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:07,914 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-10_02-15-07.log] [testng] 02:15:07,914 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ab4e390 - End of configuration. [testng] [2024-05-10 02:15:07,928] [pool-1-thread-6] Initializing /data/lee/AS_09125_050116030001_D03f00d0.DIB: [testng] 02:15:07,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:15:07,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:07,930 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-10_02-15-07.log] [testng] 02:15:07,931 |-INFO in ch.qos.logback.core.sift.SiftProcessor@601941cd - End of configuration. [testng] [2024-05-10 02:15:07,946] [pool-1-thread-5] Initializing /data/qa-7352/test/MFGTMP-PC_130509120002_B02f00o1.C01: [testng] 02:15:07,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:15:07,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:07,947 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-10_02-15-07.log] [testng] 02:15:07,947 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e9c9bfd - End of configuration. [testng] [2024-05-10 02:15:08,055] [pool-1-thread-4] Initializing /data/omar/FB03f00o1.C01: [testng] 02:15:08,055 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:15:08,055 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:08,056 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-10_02-15-08.log] [testng] 02:15:08,056 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1fac60c5 - End of configuration. [testng] [2024-05-10 02:15:08,069] [pool-1-thread-3] Initializing /data/qa-21720/AS_09125_050117190001_A14f00d0.DIB: [testng] 02:15:08,069 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:15:08,069 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:08,070 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-10_02-15-08.log] [testng] 02:15:08,070 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73caaf25 - End of configuration. [testng] [2024-05-10 02:15:08,085] [pool-1-thread-2] Initializing /data/omar/FB03f03o2.DIB: [testng] 02:15:08,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:15:08,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:15:08,086 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-10_02-15-08.log] [testng] 02:15:08,086 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b9a2fb6 - End of configuration. [testng] [2024-05-10 02:15:10,130] [pool-1-thread-7] Initializing /data/omar/FB03f00o2.C01: [testng] [2024-05-10 02:15:10,144] [pool-1-thread-2] Initializing /data/public/BBBC001/AS_09125_050118150001_A03f00d0.DIB: [testng] [2024-05-10 02:15:10,159] [pool-1-thread-12] Initializing /data/samples/sparse-plate/plate_E03f00d0.C01: [testng] [2024-05-10 02:15:10,194] [pool-1-thread-9] Initializing /data/harri/MFGTMP-PC_111018140003/MFGTMP-PC_111018140003_E04f00d0.C01: [testng] [2024-05-10 02:15:10,330] [pool-1-thread-11] Initializing /data/omar/FB03f00d1.C01: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 901, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 4 minutes 40 seconds Finished: SUCCESS