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Started by upstream project "BIOFORMATS-test-repo" build number 105 originally caused by: Started by upstream project "Trigger" build number 117 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins10741953707305006936.sh + '[' ome-tiff = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_16270_merge_ci -v /uod/idr/repos/curated/ome-tiff:/data -v /uod/idr-scratch/merge-ci/curated/ome-tiff:/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] 01:44:54,407 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:44:54,409 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 01:44:54,409 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:44:54,410 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:44:54,410 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:44:54,410 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:44:54,410 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:44:54,410 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:44:54,411 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:44:54,411 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:44:54,411 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:44:54,411 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:44:54,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:44:54,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:44:54,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:44:54,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:44:54,669 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:44:54,670 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:44:54,670 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:44:54,671 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:44:54,671 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 01:44:54,672 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 01:44:54,672 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 261 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-28 01:44:54,687] [main] java.version = 1.8.0_342 [testng] 01:44:54,693 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:44:54,693 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:54,758 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-28_01-44-54.log] [testng] 01:44:54,761 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-06-28 01:44:54,764] [main] testng.directory = /data [testng] [2024-06-28 01:44:54,765] [main] testng.configDirectory = /config [testng] [2024-06-28 01:44:54,785] [main] testng.multiplier = 1.0 [testng] [2024-06-28 01:44:54,786] [main] testng.in-memory = false [testng] [2024-06-28 01:44:54,787] [main] testng.allow-missing = false [testng] [2024-06-28 01:44:54,787] [main] user.language = en [testng] [2024-06-28 01:44:54,787] [main] user.country = ${user.country} [testng] [2024-06-28 01:44:54,787] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-06-28 01:47:30,112] [main] ---------------------------------------- [testng] [2024-06-28 01:47:30,112] [main] Total files: 4771 [testng] [2024-06-28 01:47:30,112] [main] Scan time: 155.325 s (32 ms/file) [testng] [2024-06-28 01:47:30,113] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 1455 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-28 01:54:45,758] [pool-1-thread-1] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y06/image--L03--S00--U00--V00--J00--X00--Y06--T03--Z00--C00.ome.tif: [testng] 01:54:45,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:54:45,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:45,760 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-28_01-54-45.log] [testng] 01:54:45,760 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c781f59 - End of configuration. [testng] [2024-06-28 01:54:45,805] [pool-1-thread-9] Initializing /data/peter/LA_ProtocolCombination_23.01.2012_16_29_52_1.ome.tif: [testng] 01:54:45,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:54:45,805 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:45,806 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-28_01-54-45.log] [testng] 01:54:45,807 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48db5c01 - End of configuration. [testng] [2024-06-28 01:54:46,120] [pool-1-thread-8] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X05--Y01/image--L01--S00--U00--V00--J00--X05--Y01--T01--Z00--C00.ome.tif: [testng] 01:54:46,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:54:46,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:46,121 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-28_01-54-46.log] [testng] 01:54:46,122 |-INFO in ch.qos.logback.core.sift.SiftProcessor@417d0003 - End of configuration. [testng] [2024-06-28 01:54:46,159] [pool-1-thread-7] Initializing /data/public/2007-06/single-channel.ome.tif: [testng] 01:54:46,159 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:54:46,159 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:46,160 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-28_01-54-46.log] [testng] 01:54:46,160 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27029537 - End of configuration. [testng] [2024-06-28 01:54:46,181] [pool-1-thread-6] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X01--Y03/image--L10--S00--U00--V00--J00--X01--Y03--T10--Z00--C00.ome.tif: [testng] 01:54:46,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:54:46,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:46,182 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-28_01-54-46.log] [testng] 01:54:46,182 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b729c9a - End of configuration. [testng] [2024-06-28 01:54:46,211] [pool-1-thread-5] Initializing /data/andor/iQMM_FURA_TIME123_WAVELENGTH0_0.ome.tif: [testng] 01:54:46,211 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:54:46,211 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:46,212 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-28_01-54-46.log] [testng] 01:54:46,212 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c0fb862 - End of configuration. [testng] [2024-06-28 01:54:46,239] [pool-1-thread-4] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y05/image--L10--S00--U00--V00--J00--X00--Y05--T10--Z00--C00.ome.tif: [testng] 01:54:46,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:54:46,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:46,239 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-28_01-54-46.log] [testng] 01:54:46,240 |-INFO in ch.qos.logback.core.sift.SiftProcessor@188f88d3 - End of configuration. [testng] [2024-06-28 01:54:46,266] [pool-1-thread-3] Initializing /data/andor/iQMM_FURA_TIME26_WAVELENGTH0_0.ome.tif: [testng] 01:54:46,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:54:46,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:46,267 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-28_01-54-46.log] [testng] 01:54:46,267 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ff617b1 - End of configuration. [testng] [2024-06-28 01:54:46,290] [pool-1-thread-2] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y04/image--L07--S00--U00--V00--J00--X03--Y04--T07--Z00--C00.ome.tif: [testng] 01:54:46,290 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:54:46,290 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:46,291 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-28_01-54-46.log] [testng] 01:54:46,291 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d573516 - End of configuration. [testng] [2024-06-28 01:54:46,321] [pool-1-thread-12] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y01/image--L08--S00--U00--V00--J00--X00--Y01--T08--Z00--C00.ome.tif: [testng] 01:54:46,321 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:54:46,321 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:46,322 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-28_01-54-46.log] [testng] 01:54:46,322 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b783cbd - End of configuration. [testng] [2024-06-28 01:54:46,348] [pool-1-thread-11] Initializing /data/andor/iQMM_FURA_TIME26_WAVELENGTH1_0.ome.tif: [testng] 01:54:46,348 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:54:46,348 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:46,349 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-28_01-54-46.log] [testng] 01:54:46,349 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f87e3e5 - End of configuration. [testng] [2024-06-28 01:54:46,371] [pool-1-thread-10] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X01--Y00/image--L14--S00--U00--V00--J00--X01--Y00--T14--Z00--C00.ome.tif: [testng] 01:54:46,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:54:46,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:46,372 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-28_01-54-46.log] [testng] 01:54:46,372 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75a33e51 - End of configuration. [testng] [2024-06-28 01:54:56,320] [pool-1-thread-9] Initializing /data/public/2012-06/bioformats-artificial/multi-channel-4D-series.ome.tif: [testng] [2024-06-28 01:54:56,369] [pool-1-thread-11] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X05--Y06/image--L05--S00--U00--V00--J00--X05--Y06--T05--Z00--C00.ome.tif: [testng] [2024-06-28 01:54:56,395] [pool-1-thread-5] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y03/image--L07--S00--U00--V00--J00--X03--Y03--T07--Z00--C00.ome.tif: [testng] [2024-06-28 01:54:56,422] [pool-1-thread-4] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X04--Y03/image--L04--S00--U00--V00--J00--X04--Y03--T04--Z00--C00.ome.tif: [testng] [2024-06-28 01:54:56,448] [pool-1-thread-6] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X01--Y01/image--L10--S00--U00--V00--J00--X01--Y01--T10--Z00--C00.ome.tif: [testng] [2024-06-28 01:54:56,473] [pool-1-thread-1] Initializing /data/public/2016-06/binaryonly/multifile-Z1.ome.tiff: [testng] [2024-06-28 01:54:56,485] [pool-1-thread-3] Initializing /data/andor/iQMM_FURA_TIME96_WAVELENGTH0_0.ome.tif: [testng] [2024-06-28 01:54:56,507] [pool-1-thread-2] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y04/image--L09--S00--U00--V00--J00--X02--Y04--T09--Z00--C00.ome.tif: [testng] [2024-06-28 01:54:56,534] [pool-1-thread-8] Initializing /data/public/2010-06/multi-channel-z-series-time-series.ome.tiff: [testng] [2024-06-28 01:54:56,557] [pool-1-thread-12] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X04--Y00/image--L05--S00--U00--V00--J00--X04--Y00--T05--Z00--C00.ome.tif: [testng] [2024-06-28 01:54:56,582] [pool-1-thread-10] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X04--Y00/image--L01--S00--U00--V00--J00--X04--Y00--T01--Z00--C00.ome.tif: [testng] [2024-06-28 01:54:56,610] [pool-1-thread-7] Initializing /data/andor/iQMM_FURA_TIME194_WAVELENGTH1_0.ome.tif: [testng] [2024-06-28 01:54:57,411] [pool-1-thread-3] Initializing /data/andor/iQMM_FURA_TIME90_WAVELENGTH1_0.ome.tif: [testng] [2024-06-28 01:54:57,474] [pool-1-thread-6] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y06/image--L13--S00--U00--V00--J00--X03--Y06--T13--Z00--C00.ome.tif: [testng] [2024-06-28 01:54:57,550] [pool-1-thread-2] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y03/image--L11--S00--U00--V00--J00--X03--Y03--T11--Z00--C00.ome.tif: [testng] [2024-06-28 01:54:57,598] [pool-1-thread-7] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X05--Y06/image--L10--S00--U00--V00--J00--X05--Y06--T10--Z00--C00.ome.tif: [testng] [2024-06-28 01:54:57,664] [pool-1-thread-12] Initializing /data/tubhiswtTEST/time2/lzw/lzw-tubhiswt_C1_TP1.ome.tif: [testng] [2024-06-28 01:54:57,878] [pool-1-thread-4] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y04/image--L02--S00--U00--V00--J00--X02--Y04--T02--Z00--C00.ome.tif: [testng] [2024-06-28 01:54:57,915] [pool-1-thread-10] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X06--Y02/image--L05--S00--U00--V00--J00--X06--Y02--T05--Z00--C00.ome.tif: [testng] [2024-06-28 01:54:57,941] [pool-1-thread-5] Initializing /data/curtis/mc4d-i5d.ome.tif: [testng] [2024-06-28 01:54:57,965] [pool-1-thread-1] Initializing /data/public/2016-06/bioformats-artificial/multi-channel.ome.tf8: [testng] [2024-06-28 01:54:57,982] 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/data/andor/iQMM_FURA_TIME185_WAVELENGTH0_0.ome.tif: [testng] [2024-06-28 01:59:35,389] [pool-1-thread-5] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y05/image--L14--S00--U00--V00--J00--X02--Y05--T14--Z00--C00.ome.tif: [testng] [2024-06-28 01:59:35,602] [pool-1-thread-11] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y06/image--L09--S00--U00--V00--J00--X03--Y06--T09--Z00--C00.ome.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 77115, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 24 minutes 14 seconds Finished: SUCCESS