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Started by upstream project "BIOFORMATS-test-repo" build number 66 originally caused by: Started by upstream project "Trigger" build number 74 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins16376327859383793652.sh + '[' i2i = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_9822_merge_ci -v /uod/idr/repos/curated/i2i:/data -v /uod/idr-scratch/merge-ci/curated/i2i:/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] 07:53:23,326 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 07:53:23,328 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 07:53:23,328 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 07:53:23,329 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 07:53:23,330 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 07:53:23,330 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 07:53:23,330 |-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] 07:53:23,330 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 07:53:23,331 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 07:53:23,331 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 07:53:23,331 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 07:53:23,331 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 07:53:23,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 07:53:23,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 07:53:23,686 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 07:53:23,686 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 07:53:23,702 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 07:53:23,702 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 07:53:23,703 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 07:53:23,703 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 07:53:23,703 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 07:53:23,705 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 07:53:23,705 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 374 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-17 07:53:23,721] [main] java.version = 1.8.0_342 [testng] 07:53:23,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 07:53:23,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:53:23,785 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-17_07-53-23.log] [testng] 07:53:23,787 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-05-17 07:53:23,789] [main] testng.directory = /data [testng] [2024-05-17 07:53:23,790] [main] testng.configDirectory = /config [testng] [2024-05-17 07:53:23,804] [main] testng.multiplier = 1.0 [testng] [2024-05-17 07:53:23,805] [main] testng.in-memory = false [testng] [2024-05-17 07:53:23,805] [main] testng.allow-missing = false [testng] [2024-05-17 07:53:23,805] [main] user.language = en [testng] [2024-05-17 07:53:23,805] [main] user.country = ${user.country} [testng] [2024-05-17 07:53:23,805] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-05-17 07:53:26,056] [main] ---------------------------------------- [testng] [2024-05-17 07:53:26,056] [main] Total files: 108 [testng] [2024-05-17 07:53:26,056] [main] Scan time: 2.251 s (20 ms/file) [testng] [2024-05-17 07:53:26,056] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 103 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-17 07:53:36,116] [pool-1-thread-1] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000022_491-TIRF_000.tif: [testng] 07:53:36,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 07:53:36,117 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:53:36,118 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-17_07-53-36.log] [testng] 07:53:36,118 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a827bab - End of configuration. [testng] [2024-05-17 07:53:36,178] [pool-1-thread-12] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000068_491-TIRF_000.tif: [testng] 07:53:36,179 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 07:53:36,179 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:53:36,180 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-17_07-53-36.log] [testng] 07:53:36,180 |-INFO in ch.qos.logback.core.sift.SiftProcessor@584a296d - End of configuration. [testng] [2024-05-17 07:53:36,248] [pool-1-thread-11] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000007_491-TIRF_000.tif: [testng] 07:53:36,248 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 07:53:36,248 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:53:36,249 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-17_07-53-36.log] [testng] 07:53:36,249 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41a7d569 - End of configuration. [testng] [2024-05-17 07:53:36,320] [pool-1-thread-10] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000033_491-TIRF_000.tif: [testng] 07:53:36,321 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 07:53:36,321 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:53:36,322 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-17_07-53-36.log] [testng] 07:53:36,323 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23dacfa - End of configuration. [testng] [2024-05-17 07:53:36,378] [pool-1-thread-9] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000070_491-TIRF_000.tif: [testng] 07:53:36,379 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 07:53:36,379 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:53:36,380 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-17_07-53-36.log] [testng] 07:53:36,380 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f9e35e4 - End of configuration. [testng] [2024-05-17 07:53:36,431] [pool-1-thread-8] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000032_491-TIRF_000.tif: [testng] 07:53:36,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 07:53:36,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:53:36,432 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-17_07-53-36.log] [testng] 07:53:36,433 |-INFO in ch.qos.logback.core.sift.SiftProcessor@748aa6c8 - End of configuration. [testng] [2024-05-17 07:53:36,484] [pool-1-thread-7] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000006_491-TIRF_000.tif: [testng] 07:53:36,484 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 07:53:36,484 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:53:36,485 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-17_07-53-36.log] [testng] 07:53:36,486 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bac0dd2 - End of configuration. [testng] [2024-05-17 07:53:36,536] [pool-1-thread-6] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000039_491-TIRF_000.tif: [testng] 07:53:36,536 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 07:53:36,536 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:53:36,537 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-17_07-53-36.log] [testng] 07:53:36,537 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1876b1a9 - End of configuration. [testng] [2024-05-17 07:53:36,584] [pool-1-thread-5] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000067_491-TIRF_000.tif: [testng] 07:53:36,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 07:53:36,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:53:36,585 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-17_07-53-36.log] [testng] 07:53:36,586 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2cf9ac00 - End of configuration. [testng] [2024-05-17 07:53:36,641] [pool-1-thread-4] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000013_491-TIRF_000.tif: [testng] 07:53:36,642 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 07:53:36,642 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:53:36,643 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-17_07-53-36.log] [testng] 07:53:36,643 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56760598 - End of configuration. [testng] [2024-05-17 07:53:36,704] [pool-1-thread-3] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000080_491-TIRF_000.tif: [testng] 07:53:36,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 07:53:36,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:53:36,705 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-17_07-53-36.log] [testng] 07:53:36,705 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78ab7667 - End of configuration. [testng] [2024-05-17 07:53:36,753] [pool-1-thread-2] Initializing /data/sample files/TESM_microscope/TESM_i2i_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF.i2i: [testng] 07:53:36,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 07:53:36,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:53:36,754 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-17_07-53-36.log] [testng] 07:53:36,755 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f6d1dcd - End of configuration. [testng] [2024-05-17 07:53:39,661] [pool-1-thread-2] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000073_491-TIRF_000.tif: [testng] [2024-05-17 07:53:39,710] [pool-1-thread-4] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000004_491-TIRF_000.tif: [testng] [2024-05-17 07:53:39,764] [pool-1-thread-9] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF.tif: [testng] [2024-05-17 07:53:39,859] [pool-1-thread-11] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000031_491-TIRF_000.tif: [testng] [2024-05-17 07:53:39,945] [pool-1-thread-7] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000026_491-TIRF_000.tif: [testng] [2024-05-17 07:53:40,007] [pool-1-thread-1] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000069_491-TIRF_000.tif: [testng] [2024-05-17 07:53:40,065] [pool-1-thread-3] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000003_491-TIRF_000.tif: [testng] [2024-05-17 07:53:40,136] [pool-1-thread-8] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000093_491-TIRF_000.tif: [testng] [2024-05-17 07:53:40,175] [pool-1-thread-12] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000082_491-TIRF_000.tif: [testng] [2024-05-17 07:53:40,215] [pool-1-thread-6] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000071_491-TIRF_000.tif: [testng] [2024-05-17 07:53:40,250] [pool-1-thread-10] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000050_491-TIRF_000.tif: [testng] [2024-05-17 07:53:40,299] [pool-1-thread-5] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000045_491-TIRF_000.tif: [testng] [2024-05-17 07:53:41,554] [pool-1-thread-1] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000072_491-TIRF_000.tif: [testng] [2024-05-17 07:53:41,631] [pool-1-thread-3] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000044_491-TIRF_000.tif: [testng] [2024-05-17 07:53:41,674] [pool-1-thread-10] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000001_491-TIRF_000.tif: [testng] [2024-05-17 07:53:41,712] [pool-1-thread-4] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000030_491-TIRF_000.tif: [testng] [2024-05-17 07:53:41,748] [pool-1-thread-5] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000054_491-TIRF_000.tif: [testng] [2024-05-17 07:53:41,783] [pool-1-thread-11] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000038_491-TIRF_000.tif: [testng] [2024-05-17 07:53:41,826] [pool-1-thread-12] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000094_491-TIRF_000.tif: [testng] [2024-05-17 07:53:41,864] [pool-1-thread-8] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000016_491-TIRF_000.tif: [testng] [2024-05-17 07:53:41,899] [pool-1-thread-6] Initializing /data/sample 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files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000049_491-TIRF_000.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 5459, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 32 seconds Finished: SUCCESS