Started by upstream project "BIOFORMATS-test-repo" build number 364 originally caused by: Started by upstream project "Trigger" build number 390 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/jenkins14994386180858340406.sh + '[' ome-tiff = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_58024_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 [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] 1 warning test-automated: [testng] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 00:55:10,525 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:55:10,526 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - No custom configurators were discovered as a service. [testng] 00:55:10,526 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:55:10,527 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:55:10,528 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:55:10,528 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:55:10,528 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:55:10,528 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:55:10,529 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:55:10,530 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:55:10,530 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:55:10,530 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:55:10,713 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:55:10,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:55:10,737 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:55:10,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:55:10,743 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:55:10,744 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:55:10,744 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:55:10,744 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:55:10,744 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@65c7a252 - End of configuration. [testng] 00:55:10,745 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@38cee291 - Registering current configuration as safe fallback point [testng] 00:55:10,745 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 216 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-04 00:55:10,755] [main] java.version = 11.0.16 [testng] 00:55:10,758 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:55:10,758 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:10,802 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-04_00-55-10.log] [testng] 00:55:10,803 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13d73f29 - End of configuration. [testng] [2025-03-04 00:55:10,806] [main] testng.directory = /data [testng] [2025-03-04 00:55:10,806] [main] testng.configDirectory = /config [testng] [2025-03-04 00:55:10,816] [main] testng.multiplier = 1.0 [testng] [2025-03-04 00:55:10,817] [main] testng.in-memory = false [testng] [2025-03-04 00:55:10,817] [main] testng.allow-missing = false [testng] [2025-03-04 00:55:10,818] [main] user.language = en [testng] [2025-03-04 00:55:10,818] [main] user.country = ${user.country} [testng] [2025-03-04 00:55:10,818] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-04 00:59:43,159] [main] ---------------------------------------- [testng] [2025-03-04 00:59:43,160] [main] Total files: 4771 [testng] [2025-03-04 00:59:43,160] [main] Scan time: 272.341 s (57 ms/file) [testng] [2025-03-04 00:59:43,160] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 1455 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-04 01:40:40,612] [pool-1-thread-1] Initializing /data/ruben/experiment--2009_10_27_15_43_34/slide--S00/chamber--U00--V00/field--X01--Y00/image--L00--S00--U00--V00--J00--X01--Y00--T00--Z00--C00.ome.tif: [testng] 01:40:40,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:40:40,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:40,615 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-04_01-40-40.log] [testng] 01:40:40,616 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31c2bf2b - End of configuration. [testng] [2025-03-04 01:40:41,143] [pool-1-thread-12] Initializing /data/jared/x_noisy.ome.tif: [testng] 01:40:41,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:40:41,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:41,143 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-04_01-40-41.log] [testng] 01:40:41,144 |-INFO in ch.qos.logback.core.sift.SiftProcessor@574474c8 - End of configuration. [testng] [2025-03-04 01:40:41,691] [pool-1-thread-11] Initializing /data/andor/iQMM_FURA_TIME169_WAVELENGTH1_0.ome.tif: [testng] 01:40:41,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:40:41,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:41,692 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-04_01-40-41.log] [testng] 01:40:41,692 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6517fd2c - End of configuration. [testng] [2025-03-04 01:40:42,503] [pool-1-thread-10] Initializing /data/scott/4.2_roundTrip/exported_4.2.ome.tif: [testng] 01:40:42,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:40:42,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:42,504 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-04_01-40-42.log] [testng] 01:40:42,504 |-INFO in ch.qos.logback.core.sift.SiftProcessor@504daf15 - End of configuration. [testng] [2025-03-04 01:40:43,088] [pool-1-thread-9] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X04--Y00/image--L03--S00--U00--V00--J00--X04--Y00--T03--Z00--C00.ome.tif: [testng] 01:40:43,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:40:43,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:43,089 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-04_01-40-43.log] [testng] 01:40:43,090 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10f7d22e - End of configuration. [testng] [2025-03-04 01:40:43,837] [pool-1-thread-8] Initializing /data/andor/iQMM_FURA_TIME9_WAVELENGTH0_0.ome.tif: [testng] 01:40:43,837 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:40:43,837 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:43,837 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-04_01-40-43.log] [testng] 01:40:43,838 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43499293 - End of configuration. [testng] [2025-03-04 01:40:44,490] [pool-1-thread-7] Initializing /data/olaf/OmeTest2.ome.tiff: [testng] 01:40:44,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:40:44,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:44,491 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-04_01-40-44.log] [testng] 01:40:44,491 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d7a7f0b - End of configuration. [testng] [2025-03-04 01:40:45,125] [pool-1-thread-6] Initializing /data/glen/OMETiff Slidebook donotopen/Capture 2 - Position 1_XY1306537975_Z00_T002_C1.tiff: [testng] 01:40:45,125 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:40:45,125 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:45,126 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-04_01-40-45.log] [testng] 01:40:45,126 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a42a0f7 - End of configuration. [testng] [2025-03-04 01:40:46,039] [pool-1-thread-5] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X01--Y01/image--L03--S00--U00--V00--J00--X01--Y01--T03--Z00--C00.ome.tif: [testng] 01:40:46,040 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:40:46,040 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:46,040 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-04_01-40-46.log] [testng] 01:40:46,041 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53f99f79 - End of configuration. [testng] [2025-03-04 01:40:46,644] [pool-1-thread-4] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X04--Y05/image--L10--S00--U00--V00--J00--X04--Y05--T10--Z00--C00.ome.tif: [testng] 01:40:46,644 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:40:46,644 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:46,644 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-04_01-40-46.log] [testng] 01:40:46,645 |-INFO in ch.qos.logback.core.sift.SiftProcessor@95bc746 - End of configuration. [testng] [2025-03-04 01:40:47,293] [pool-1-thread-3] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y05/image--L01--S00--U00--V00--J00--X02--Y05--T01--Z00--C00.ome.tif: [testng] 01:40:47,294 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:40:47,294 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:47,294 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-04_01-40-47.log] [testng] 01:40:47,295 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c79d3d7 - End of configuration. [testng] [2025-03-04 01:40:47,943] [pool-1-thread-2] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y05/image--L08--S00--U00--V00--J00--X02--Y05--T08--Z00--C00.ome.tif: [testng] 01:40:47,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:40:47,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:40:47,944 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-04_01-40-47.log] [testng] 01:40:47,945 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8691bb0 - End of configuration. [testng] [2025-03-04 01:40:54,101] [pool-1-thread-12] Initializing /data/andor/iQMM_FURA_TIME5_WAVELENGTH0_0.ome.tif: [testng] [2025-03-04 01:40:55,189] [pool-1-thread-7] Initializing /data/andor/iQMM_FURA_TIME180_WAVELENGTH1_0.ome.tif: [testng] [2025-03-04 01:40:55,955] [pool-1-thread-10] Initializing /data/public/2010-04/multi-channel-z-series.ome.tiff: [testng] [2025-03-04 01:40:57,016] [pool-1-thread-6] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X06--Y06/image--L12--S00--U00--V00--J00--X06--Y06--T12--Z00--C00.ome.tif: [testng] [2025-03-04 01:40:59,595] [pool-1-thread-3] Initializing /data/andor/iQMM_FURA_TIME147_WAVELENGTH0_0.ome.tif: [testng] [2025-03-04 01:41:00,510] [pool-1-thread-2] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X06--Y02/image--L08--S00--U00--V00--J00--X06--Y02--T08--Z00--C00.ome.tif: [testng] [2025-03-04 01:41:01,167] [pool-1-thread-9] Initializing /data/andor/iQMM_FURA_TIME174_WAVELENGTH0_0.ome.tif: [testng] [2025-03-04 01:41:01,758] [pool-1-thread-1] Initializing /data/public/2016-06/bioformats-artificial/z-series.ome.tif: [testng] [2025-03-04 01:41:02,306] [pool-1-thread-4] Initializing /data/andor/iQMM_FURA_TIME140_WAVELENGTH0_0.ome.tif: [testng] [2025-03-04 01:41:02,827] [pool-1-thread-5] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X06--Y03/image--L03--S00--U00--V00--J00--X06--Y03--T03--Z00--C00.ome.tif: [testng] [2025-03-04 01:41:03,297] [pool-1-thread-11] Initializing /data/andor/iQMM_FURA_TIME173_WAVELENGTH0_0.ome.tif: [testng] [2025-03-04 01:41:03,829] [pool-1-thread-8] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y01/image--L08--S00--U00--V00--J00--X03--Y01--T08--Z00--C00.ome.tif: [testng] [2025-03-04 01:41:06,346] [pool-1-thread-10] Initializing 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/data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y01/image--L05--S00--U00--V00--J00--X03--Y01--T05--Z00--C00.ome.tif: [testng] [2025-03-04 01:41:15,033] [pool-1-thread-8] Initializing /data/andor/iQMM_FURA_TIME192_WAVELENGTH1_0.ome.tif: [testng] [2025-03-04 01:41:15,661] [pool-1-thread-5] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y05/image--L00--S00--U00--V00--J00--X02--Y05--T00--Z00--C00.ome.tif: [testng] [2025-03-04 01:41:16,143] [pool-1-thread-3] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X01--Y05/image--L09--S00--U00--V00--J00--X01--Y05--T09--Z00--C00.ome.tif: [testng] [2025-03-04 01:41:16,699] [pool-1-thread-11] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y04/image--L14--S00--U00--V00--J00--X03--Y04--T14--Z00--C00.ome.tif: [testng] [2025-03-04 01:41:17,151] [pool-1-thread-4] Initializing 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/data/andor/iQMM_FURA_TIME96_WAVELENGTH0_0.ome.tif: [testng] [2025-03-04 02:29:05,962] [pool-1-thread-6] Initializing /data/public/2016-06/bioformats-artificial/time-series.ome.tif: [testng] [2025-03-04 02:29:08,313] [pool-1-thread-10] Initializing /data/andor/iQMM_FURA_TIME87_WAVELENGTH0_0.ome.tif: [testng] [2025-03-04 02:29:12,511] [pool-1-thread-7] Initializing /data/prairie/ZSeries-12062007-1400-096/ZSeries-12062007-1400-096.xml: [testng] 03:49:47,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:49:47,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:49:47,268 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-04_03-49-47.log] [testng] 03:49:47,269 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55ccd38a - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 77115, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 174 minutes 40 seconds Finished: SUCCESS