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Started by upstream project "BIOFORMATS-test-repo" build number 112 originally caused by: Started by upstream project "Trigger" build number 125 originally caused by: Started by timer 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/jenkins17968605530280288348.sh + '[' i2i = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_17366_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] 01:21:43,642 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:21:43,644 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 01:21:43,644 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:21:43,645 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:21:43,646 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:21:43,646 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:21:43,646 |-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] 01:21:43,646 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:21:43,647 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:21:43,647 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:21:43,647 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:21:43,647 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:21:43,957 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:21:43,957 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:21:43,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:21:43,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:21:44,009 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:21:44,009 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:21:44,009 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:21:44,010 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:21:44,010 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 01:21:44,012 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 01:21:44,012 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 365 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-05 01:21:44,029] [main] java.version = 1.8.0_342 [testng] 01:21:44,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:21:44,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:44,087 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-05_01-21-44.log] [testng] 01:21:44,089 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-07-05 01:21:44,091] [main] testng.directory = /data [testng] [2024-07-05 01:21:44,092] [main] testng.configDirectory = /config [testng] [2024-07-05 01:21:44,105] [main] testng.multiplier = 1.0 [testng] [2024-07-05 01:21:44,105] [main] testng.in-memory = false [testng] [2024-07-05 01:21:44,105] [main] testng.allow-missing = false [testng] [2024-07-05 01:21:44,106] [main] user.language = en [testng] [2024-07-05 01:21:44,106] [main] user.country = ${user.country} [testng] [2024-07-05 01:21:44,106] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-07-05 01:21:45,933] [main] ---------------------------------------- [testng] [2024-07-05 01:21:45,933] [main] Total files: 108 [testng] [2024-07-05 01:21:45,933] [main] Scan time: 1.827 s (16 ms/file) [testng] [2024-07-05 01:21:45,933] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 103 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-05 01:21:55,906] [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] 01:21:55,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:21:55,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:55,908 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-05_01-21-55.log] [testng] 01:21:55,908 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27d174e8 - End of configuration. [testng] [2024-07-05 01:21:55,971] [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] 01:21:55,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:21:55,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:55,974 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-05_01-21-55.log] [testng] 01:21:55,974 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38dd4612 - End of configuration. [testng] [2024-07-05 01:21:56,060] [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] 01:21:56,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:21:56,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:56,061 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-05_01-21-56.log] [testng] 01:21:56,062 |-INFO in ch.qos.logback.core.sift.SiftProcessor@673cd323 - End of configuration. [testng] [2024-07-05 01:21:56,184] [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] 01:21:56,185 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:21:56,185 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:56,186 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-05_01-21-56.log] [testng] 01:21:56,186 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2eae8ec3 - End of configuration. [testng] [2024-07-05 01:21:56,264] [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] 01:21:56,265 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:21:56,265 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:56,266 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-05_01-21-56.log] [testng] 01:21:56,267 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4035c0b8 - End of configuration. [testng] [2024-07-05 01:21:56,344] [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] 01:21:56,344 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:21:56,344 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:56,345 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-05_01-21-56.log] [testng] 01:21:56,345 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7df234ca - End of configuration. [testng] [2024-07-05 01:21:56,393] [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] 01:21:56,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:21:56,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:56,394 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-05_01-21-56.log] [testng] 01:21:56,394 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12a31ee1 - End of configuration. [testng] [2024-07-05 01:21:56,438] [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] 01:21:56,439 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:21:56,439 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:56,440 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-05_01-21-56.log] [testng] 01:21:56,440 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51c82ca6 - End of configuration. [testng] [2024-07-05 01:21:56,496] [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] 01:21:56,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:21:56,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:56,498 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-05_01-21-56.log] [testng] 01:21:56,498 |-INFO in ch.qos.logback.core.sift.SiftProcessor@335aa2e8 - End of configuration. [testng] [2024-07-05 01:21:56,555] [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] 01:21:56,555 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:21:56,556 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:56,557 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-05_01-21-56.log] [testng] 01:21:56,558 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2cded989 - End of configuration. [testng] [2024-07-05 01:21:56,644] [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] 01:21:56,645 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:21:56,645 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:56,646 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-05_01-21-56.log] [testng] 01:21:56,647 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c258cd8 - End of configuration. [testng] [2024-07-05 01:21:56,738] [pool-1-thread-2] Initializing /data/sample files/TESM_microscope/TESM_i2i_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF.i2i: [testng] 01:21:56,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:21:56,739 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:56,739 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-05_01-21-56.log] [testng] 01:21:56,740 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a79f533 - End of configuration. [testng] [2024-07-05 01:21:59,731] [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] [2024-07-05 01:21:59,789] [pool-1-thread-5] 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] [2024-07-05 01:21:59,834] [pool-1-thread-9] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF.tif: [testng] [2024-07-05 01:21:59,939] [pool-1-thread-6] 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] [2024-07-05 01:22:00,022] [pool-1-thread-4] 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] [2024-07-05 01:22:00,116] [pool-1-thread-10] 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] [2024-07-05 01:22:00,223] [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] [2024-07-05 01:22:00,290] [pool-1-thread-7] 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] [2024-07-05 01:22:00,339] [pool-1-thread-11] 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] [2024-07-05 01:22:00,372] [pool-1-thread-1] 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] [2024-07-05 01:22:00,410] [pool-1-thread-8] 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] [2024-07-05 01:22:00,451] [pool-1-thread-12] 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] [2024-07-05 01:22:02,259] [pool-1-thread-4] 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] [2024-07-05 01:22:02,304] [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] [2024-07-05 01:22:02,362] [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] [2024-07-05 01:22:02,412] [pool-1-thread-12] 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] [2024-07-05 01:22:02,461] [pool-1-thread-8] 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] [2024-07-05 01:22:02,539] [pool-1-thread-7] 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] [2024-07-05 01:22:02,600] [pool-1-thread-1] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000077_491-TIRF_000.tif: [testng] [2024-07-05 01:22:02,653] [pool-1-thread-11] Initializing /data/sample files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000083_491-TIRF_000.tif: [testng] [2024-07-05 01:22:02,737] [pool-1-thread-10] Initializing /data/sample 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files/TESM_microscope/TESM_tiff_sampleFiles/2013-06-13-U2OS_MFR_Test_0_491-TIRF/img_000000036_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: 36 seconds Finished: SUCCESS