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Started by upstream project "BIOFORMATS-test-repo" build number 390 originally caused by: Started by upstream project "Trigger" build number 414 originally caused by: Started by user devspace Restarted from build #413, stage Bio-Formats Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@10 [BIOFORMATS-test-folder@10] $ /bin/bash -xe /tmp/jenkins15002680665827522719.sh + '[' samples = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_61682_merge_ci -v /uod/idr/repos/curated/samples:/data -v /uod/idr-scratch/merge-ci/curated/samples:/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] 01:09:14,847 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 01:09:14,849 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - No custom configurators were discovered as a service. [testng] 01:09:14,849 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:09:14,851 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:09:14,852 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:09:14,852 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:09:14,853 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:09:14,853 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:09:14,853 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:09:14,854 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:09:14,855 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:09:14,855 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:09:15,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:09:15,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:09:15,109 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:09:15,109 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:09:15,115 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:09:15,116 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:09:15,116 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:09:15,116 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:09:15,116 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@65c7a252 - End of configuration. [testng] 01:09:15,117 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@38cee291 - Registering current configuration as safe fallback point [testng] 01:09:15,117 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 264 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-25 01:09:15,130] [main] java.version = 11.0.16 [testng] 01:09:15,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:09:15,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:09:15,202 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-25_01-09-15.log] [testng] 01:09:15,204 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13d73f29 - End of configuration. [testng] [2025-03-25 01:09:15,207] [main] testng.directory = /data [testng] [2025-03-25 01:09:15,207] [main] testng.configDirectory = /config [testng] [2025-03-25 01:09:15,217] [main] testng.multiplier = 1.0 [testng] [2025-03-25 01:09:15,218] [main] testng.in-memory = false [testng] [2025-03-25 01:09:15,219] [main] testng.allow-missing = false [testng] [2025-03-25 01:09:15,219] [main] user.language = en [testng] [2025-03-25 01:09:15,219] [main] user.country = ${user.country} [testng] [2025-03-25 01:09:15,219] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-25 01:11:36,373] [main] ---------------------------------------- [testng] [2025-03-25 01:11:36,373] [main] Total files: 165 [testng] [2025-03-25 01:11:36,373] [main] Scan time: 141.154 s (855 ms/file) [testng] [2025-03-25 01:11:36,373] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 60 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-25 01:15:13,898] [pool-1-thread-1] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] 01:15:13,898 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:15:13,899 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:13,901 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-25_01-15-13.log] [testng] 01:15:13,901 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35048dc9 - End of configuration. [testng] [2025-03-25 01:15:14,325] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 01:15:14,325 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:15:14,325 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:14,326 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-25_01-15-14.log] [testng] 01:15:14,326 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27949bae - End of configuration. [testng] [2025-03-25 01:15:14,664] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] 01:15:14,664 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:15:14,664 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:14,665 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-25_01-15-14.log] [testng] 01:15:14,666 |-INFO in ch.qos.logback.core.sift.SiftProcessor@597cc3e7 - End of configuration. [testng] [2025-03-25 01:15:15,113] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 01:15:15,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:15:15,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:15,114 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-25_01-15-15.log] [testng] 01:15:15,115 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d08340f - End of configuration. [testng] [2025-03-25 01:15:17,158] [pool-1-thread-9] Initializing /data/ome/compressed2ChZ.lsm: [testng] 01:15:17,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:15:17,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:17,159 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-25_01-15-17.log] [testng] 01:15:17,159 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21eb1aa3 - End of configuration. [testng] [2025-03-25 01:15:19,330] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 01:15:19,331 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:15:19,331 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:19,331 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-25_01-15-19.log] [testng] 01:15:19,332 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d0cbf14 - End of configuration. [testng] [2025-03-25 01:15:21,485] [pool-1-thread-7] Initializing /data/ome/anusgfpzs.lsm: [testng] 01:15:21,486 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:15:21,486 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:21,486 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-25_01-15-21.log] [testng] 01:15:21,487 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7cfa8e5f - End of configuration. [testng] [2025-03-25 01:15:23,600] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes2.ppm: [testng] 01:15:23,600 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:15:23,600 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:23,601 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-25_01-15-23.log] [testng] 01:15:23,601 |-INFO in ch.qos.logback.core.sift.SiftProcessor@450a18d5 - End of configuration. [testng] [2025-03-25 01:15:23,904] [pool-1-thread-5] Initializing /data/ome/Adultmidsection.lsm: [testng] 01:15:23,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:15:23,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:23,905 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-25_01-15-23.log] [testng] 01:15:23,906 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a5bbb20 - End of configuration. [testng] [2025-03-25 01:15:25,941] [pool-1-thread-4] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] 01:15:25,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:15:25,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:25,943 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-25_01-15-25.log] [testng] 01:15:25,943 |-INFO in ch.qos.logback.core.sift.SiftProcessor@485e6c9e - End of configuration. [testng] [2025-03-25 01:15:26,298] [pool-1-thread-3] Initializing /data/ome/CHOBI_d3d.dv: [testng] 01:15:26,298 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:15:26,298 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:26,299 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-25_01-15-26.log] [testng] 01:15:26,300 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3db96b21 - End of configuration. [testng] [2025-03-25 01:15:26,901] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 01:15:26,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:15:26,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:15:26,902 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-25_01-15-26.log] [testng] 01:15:26,902 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30624b25 - End of configuration. [testng] [2025-03-25 01:15:32,875] [pool-1-thread-6] Initializing /data/openjpeg/Rome.ppm: [testng] [2025-03-25 01:15:33,437] [pool-1-thread-2] Initializing /data/ome/cb_1.r3d: [testng] [2025-03-25 01:15:34,389] [pool-1-thread-12] Initializing /data/openjpeg/Facade.bmp: [testng] [2025-03-25 01:15:34,980] [pool-1-thread-3] Initializing /data/openjpeg/Facade.pnm: [testng] [2025-03-25 01:15:35,830] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2025-03-25 01:15:38,162] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2025-03-25 01:15:38,939] [pool-1-thread-11] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2025-03-25 01:15:39,256] [pool-1-thread-1] Initializing /data/ome/embryo.lsm: [testng] [2025-03-25 01:15:41,848] [pool-1-thread-8] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2025-03-25 01:15:42,241] [pool-1-thread-7] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2025-03-25 01:15:43,955] [pool-1-thread-5] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2025-03-25 01:15:45,318] [pool-1-thread-10] Initializing /data/ome/011B1_Morph.HTD: [testng] [2025-03-25 01:15:47,385] [pool-1-thread-2] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2025-03-25 01:15:48,662] [pool-1-thread-9] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2025-03-25 01:15:51,288] [pool-1-thread-4] Initializing /data/TAABA/TAABA.pattern: [testng] [2025-03-25 01:16:55,860] [pool-1-thread-3] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2025-03-25 01:16:57,852] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2025-03-25 01:16:59,522] [pool-1-thread-11] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2025-03-25 01:17:00,389] [pool-1-thread-8] Initializing /data/ARFTest/ARFTest.arf: [testng] [2025-03-25 01:17:01,830] [pool-1-thread-6] Initializing /data/ome/worm.tiff: [testng] [2025-03-25 01:17:07,011] [pool-1-thread-1] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2025-03-25 01:17:09,524] [pool-1-thread-12] Initializing /data/openjpeg/Rome.jp2: [testng] [2025-03-25 01:17:11,220] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2025-03-25 01:17:11,626] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2025-03-25 01:17:12,022] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2025-03-25 01:17:12,900] [pool-1-thread-11] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2025-03-25 01:17:16,439] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2025-03-25 01:17:19,112] [pool-1-thread-3] Initializing /data/ome/tiffany.color.tiff: [testng] [2025-03-25 01:17:26,796] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2025-03-25 01:17:27,896] [pool-1-thread-7] Initializing /data/openjpeg/Rome.bmp: [testng] [2025-03-25 01:17:28,387] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2025-03-25 01:17:28,855] [pool-1-thread-2] Initializing /data/ome/654Atemp.stk: [testng] [2025-03-25 01:17:37,561] [pool-1-thread-12] Initializing /data/ome/C1.lsm: [testng] [2025-03-25 01:17:40,882] [pool-1-thread-8] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2025-03-25 01:17:44,709] [pool-1-thread-7] Initializing /data/sdub/sdub.pattern: [testng] [2025-03-25 01:18:04,751] [pool-1-thread-6] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2025-03-25 01:18:06,529] [pool-1-thread-11] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2025-03-25 01:18:07,513] [pool-1-thread-5] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2025-03-25 01:18:12,010] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2025-03-25 01:18:15,017] [pool-1-thread-12] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2025-03-25 01:18:19,286] [pool-1-thread-3] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2025-03-25 01:18:27,401] [pool-1-thread-5] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2025-03-25 01:18:31,846] [pool-1-thread-8] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2025-03-25 01:18:37,192] [pool-1-thread-2] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2025-03-25 01:18:47,048] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2025-03-25 01:18:52,334] [pool-1-thread-11] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2025-03-25 01:18:56,245] [pool-1-thread-12] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2025-03-25 01:19:00,980] [pool-1-thread-6] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3180, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 18 minutes 1 second Finished: SUCCESS