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Started by upstream project "BIOFORMATS-test-repo" build number 115 originally caused by: Started by upstream project "Trigger" build number 128 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins13098326986984854997.sh + '[' leica-lif = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_18008_merge_ci -v /uod/idr/repos/curated/leica-lif:/data -v /uod/idr-scratch/merge-ci/curated/leica-lif:/config snoopycrimecop/bioformats:merge_ci -Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR 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] 02:43:56,042 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:43:56,044 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 02:43:56,044 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:43:56,045 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:43:56,045 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:43:56,045 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:43:56,046 |-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] 02:43:56,046 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:43:56,046 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:43:56,047 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:43:56,047 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:43:56,047 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:43:56,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:43:56,310 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:43:56,343 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:43:56,344 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:43:56,354 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:43:56,354 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:43:56,355 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:43:56,355 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:43:56,355 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 02:43:56,356 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 02:43:56,356 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 310 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-08 02:43:56,369] [main] java.version = 1.8.0_342 [testng] 02:43:56,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:43:56,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:43:56,425 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-08_02-43-56.log] [testng] 02:43:56,427 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-07-08 02:43:56,432] [main] testng.directory = /data [testng] [2024-07-08 02:43:56,432] [main] testng.configDirectory = /config [testng] [2024-07-08 02:43:56,459] [main] testng.multiplier = 1.0 [testng] [2024-07-08 02:43:56,459] [main] testng.in-memory = false [testng] [2024-07-08 02:43:56,459] [main] testng.allow-missing = false [testng] [2024-07-08 02:43:56,460] [main] user.language = fr [testng] [2024-07-08 02:43:56,460] [main] user.country = FR [testng] [2024-07-08 02:43:56,460] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-07-08 02:47:50,013] [main] ---------------------------------------- [testng] [2024-07-08 02:47:50,013] [main] Total files: 402 [testng] [2024-07-08 02:47:50,013] [main] Scan time: 233.552 s (580 ms/file) [testng] [2024-07-08 02:47:50,013] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 266 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-08 02:49:42,679] [pool-1-thread-1] Initializing /data/kota/int_ok.lif: [testng] 02:49:42,679 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:49:42,679 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:42,680 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-08_02-49-42.log] [testng] 02:49:42,681 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7bba9e6d - End of configuration. [testng] [2024-07-08 02:49:42,742] [pool-1-thread-12] Initializing /data/andrew/New XZY LIF Upload/XZY Stacks.lif: [testng] 02:49:42,742 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:49:42,742 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:42,743 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-08_02-49-42.log] [testng] 02:49:42,743 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bf4bc31 - End of configuration. [testng] [2024-07-08 02:49:42,800] [pool-1-thread-11] Initializing /data/qa-4791/TestFlorianDescription2.lif: [testng] 02:49:42,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:49:42,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:42,801 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-08_02-49-42.log] [testng] 02:49:42,801 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c1a7bb2 - End of configuration. [testng] [2024-07-08 02:49:42,818] [pool-1-thread-10] Initializing /data/andrew/Series 68 TIFFs/Series068_t6_y6.tif: [testng] 02:49:42,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:49:42,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:42,819 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-08_02-49-42.log] [testng] 02:49:42,819 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40c7b72a - End of configuration. [testng] [2024-07-08 02:49:42,867] [pool-1-thread-9] Initializing /data/andrew/Series 68 TIFFs/Series068_t6_y4.tif: [testng] 02:49:42,867 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:49:42,867 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:42,868 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-08_02-49-42.log] [testng] 02:49:42,868 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ffdd41d - End of configuration. [testng] [2024-07-08 02:49:42,914] [pool-1-thread-8] Initializing /data/public/seanwarren/150519_FRAP_test_ROIs_chromagreen/FRAP002_5um.png: [testng] 02:49:42,914 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:49:42,914 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:42,915 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-08_02-49-42.log] [testng] 02:49:42,916 |-INFO in ch.qos.logback.core.sift.SiftProcessor@419a1eed - End of configuration. [testng] [2024-07-08 02:49:42,930] [pool-1-thread-7] Initializing /data/melissa/roi-test-1.xml: [testng] 02:49:42,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:49:42,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:42,931 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-08_02-49-42.log] [testng] 02:49:42,932 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65f0341d - End of configuration. [testng] [2024-07-08 02:49:42,955] [pool-1-thread-6] Initializing /data/sebastian/sebHaase2.lif: [testng] 02:49:42,955 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:49:42,956 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:42,956 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-08_02-49-42.log] [testng] 02:49:42,956 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e7eb5ca - End of configuration. [testng] [2024-07-08 02:49:43,025] [pool-1-thread-5] Initializing /data/public/seanwarren/150519_FRAP_test_ROIs_chromagreen/FRAP003_10um.png: [testng] 02:49:43,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:49:43,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:43,026 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-08_02-49-43.log] [testng] 02:49:43,026 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c9fcb28 - End of configuration. [testng] [2024-07-08 02:49:43,035] [pool-1-thread-4] Initializing /data/pki/20111116preCK50.lif: [testng] 02:49:43,035 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:49:43,035 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:43,036 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-08_02-49-43.log] [testng] 02:49:43,036 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a2496a4 - End of configuration. [testng] [2024-07-08 02:49:43,110] [pool-1-thread-3] Initializing /data/andrew/Series 68 TIFFs/Series068_t5_y0.tif: [testng] 02:49:43,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:49:43,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:43,111 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-08_02-49-43.log] [testng] 02:49:43,112 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19ef8c17 - End of configuration. [testng] [2024-07-08 02:49:43,196] [pool-1-thread-2] Initializing /data/andrew/Series 68 Multi from Importer.tif: [testng] 02:49:43,196 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:49:43,196 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:43,196 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-08_02-49-43.log] [testng] 02:49:43,197 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28de1821 - End of configuration. [testng] [2024-07-08 02:49:46,283] [pool-1-thread-11] Initializing /data/andrew/Series 68 TIFFs/Series068_t9_y5.tif: [testng] [2024-07-08 02:49:46,312] [pool-1-thread-12] Initializing /data/tony/Celegeansexp01.lif: [testng] [2024-07-08 02:49:46,369] [pool-1-thread-10] Initializing /data/andrew/New XZY LIF Upload/Right Order/XZY Stacks Right Order Ch2.avi: [testng] [2024-07-08 02:49:46,513] [pool-1-thread-9] Initializing /data/andrew/New XZY LIF Upload/Wrong Order/XZY Stacks Wrong Order Ch2.avi: [testng] [2024-07-08 02:49:46,538] [pool-1-thread-3] Initializing /data/jcb/201007044/Figure 4D - F505.lif: [testng] [2024-07-08 02:49:46,552] [pool-1-thread-7] Initializing /data/dirk/Mag-test.lif: [testng] [2024-07-08 02:49:46,702] [pool-1-thread-6] Initializing /data/melissa/Series001_z0.tif: [testng] [2024-07-08 02:49:46,744] [pool-1-thread-5] Initializing /data/tony/OPN_cy3_dapi_trab.lif: [testng] [2024-07-08 02:49:46,793] [pool-1-thread-8] Initializing /data/andrew/Series 68 TIFFs/Series068_t7_y7.tif: [testng] [2024-07-08 02:49:47,015] [pool-1-thread-3] Initializing /data/andrew/Series 68 TIFFs/Series068_t7_y5.tif: [testng] [2024-07-08 02:49:47,180] [pool-1-thread-10] Initializing /data/andrew/Series 68 TIFFs/Series068_t0_y1.tif: [testng] [2024-07-08 02:49:47,227] [pool-1-thread-9] Initializing /data/public/seanwarren/150519_FRAP_test_ROIs_chromagreen/FRAP001_2_5um.png: [testng] [2024-07-08 02:49:47,330] [pool-1-thread-11] Initializing /data/qa-7273/5-17 Hypoxia.lif: [testng] [2024-07-08 02:49:47,556] [pool-1-thread-6] Initializing /data/andrew/FRAP_Test_250708.lif: [testng] [2024-07-08 02:49:47,766] [pool-1-thread-7] Initializing /data/jerome/E346_316.lif: [testng] [2024-07-08 02:49:47,931] [pool-1-thread-1] Initializing /data/oliver/Single Channel Measurements.lif: [testng] [2024-07-08 02:49:48,008] [pool-1-thread-8] Initializing /data/stefan/Experiment.lif: [testng] [2024-07-08 02:49:48,207] [pool-1-thread-3] Initializing /data/andrew/Series 68 TIFFs/Series068_t5_y3.tif: [testng] [2024-07-08 02:49:48,324] [pool-1-thread-10] Initializing /data/christian/20090323fluoresceinRPMI.lif: [testng] [2024-07-08 02:49:48,479] [pool-1-thread-9] Initializing /data/andrew/Series 68 TIFFs/Series068_t8_y6.tif: [testng] [2024-07-08 02:49:48,745] [pool-1-thread-5] Initializing /data/fabrice/09-10-23 Tete de mouche.lif: [testng] [2024-07-08 02:49:49,034] [pool-1-thread-10] Initializing /data/qa-10980/Day 2 Chitin Kan.lif: [testng] [2024-07-08 02:49:49,210] [pool-1-thread-3] Initializing /data/romain/tile 002.lif: [testng] [2024-07-08 02:49:49,425] [pool-1-thread-5] Initializing /data/alex/2010-11-29-test-for-OME.lif: [testng] [2024-07-08 02:49:49,464] [pool-1-thread-9] Initializing /data/vytas/Series008_t000_ch00.tif: [testng] [2024-07-08 02:49:49,994] [pool-1-thread-8] Initializing /data/schek/Experiment_001.lif: [testng] [2024-07-08 02:49:50,225] [pool-1-thread-5] Initializing /data/andrew/Series 68 TIFFs/Series068_t2_y4.tif: [testng] [2024-07-08 02:49:51,101] [pool-1-thread-5] Initializing /data/jcb/JCB 201203109/FIG 2D STAT3-EYFP CNTF.lif: [testng] [2024-07-08 02:49:51,216] [pool-1-thread-2] Initializing /data/stefan/spe.lif: [testng] [2024-07-08 02:49:51,318] [pool-1-thread-12] Initializing /data/andrew/Series 68 TIFFs/Series068_t9_y2.tif: [testng] [2024-07-08 02:49:51,914] [pool-1-thread-12] Initializing /data/vytas/LIFtest.lif: [testng] [2024-07-08 02:49:52,013] [pool-1-thread-5] Initializing /data/andrew/Series 68 TIFFs/Series068_t2_y2.tif: [testng] [2024-07-08 02:49:52,172] [pool-1-thread-2] Initializing /data/andrew/Series 68 TIFFs/Series068_t8_y1.tif: [testng] [2024-07-08 02:49:52,396] [pool-1-thread-12] Initializing /data/jerome/E345_312.lif: [testng] [2024-07-08 02:49:52,837] [pool-1-thread-5] Initializing /data/andrew/Series 68 TIFFs/Series068_t8_y0.tif: [testng] [2024-07-08 02:49:52,884] [pool-1-thread-7] Initializing /data/leon/leon002.lif: [testng] [2024-07-08 02:49:52,940] [pool-1-thread-2] Initializing /data/melissa/roi-test-1.lif: [testng] [2024-07-08 02:49:53,340] [pool-1-thread-7] Initializing /data/andrew/LIF Lambda/Montage of Alexa 488 Lambda.tif: [testng] [2024-07-08 02:49:53,417] [pool-1-thread-2] Initializing /data/matthias/ms-first tests.lif: [testng] [2024-07-08 02:49:53,646] [pool-1-thread-5] Initializing /data/andrew/LIF Lambda/Lambda 1.lif: [testng] [2024-07-08 02:49:53,857] [pool-1-thread-7] Initializing /data/andrew/Series 68 TIFFs/Series068_t3_y6.tif: [testng] [2024-07-08 02:49:54,067] [pool-1-thread-1] Initializing /data/pki/RA4 P3 x63.lif: [testng] [2024-07-08 02:49:54,495] [pool-1-thread-9] Initializing /data/andrew/Series 68 TIFFs/Series068_t7_y4.tif: [testng] [2024-07-08 02:49:54,753] [pool-1-thread-7] Initializing /data/andrew/New XZY LIF Upload/Right Order/XZY Stacks Right Order Ch1.avi: [testng] [2024-07-08 02:49:55,094] [pool-1-thread-1] Initializing /data/andrew/Series 68 TIFFs/Series068_t2_y8.tif: [testng] [2024-07-08 02:49:55,149] 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[2024-07-08 02:50:44,897] [pool-1-thread-5] Initializing /data/fabrice/new/UL66 bicolore stacks + merge.lif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 14098, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 9 minutes 51 seconds Finished: SUCCESS