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Started by upstream project "BIOFORMATS-test-repo" build number 210 originally caused by: Started by upstream project "Trigger" build number 236 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/jenkins6389213810109656586.sh + '[' simplepci = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_33334_merge_ci -v /uod/idr/repos/curated/simplepci:/data -v /uod/idr-scratch/merge-ci/curated/simplepci:/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] 02:00:59,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:00:59,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:01:00,000 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:01:00,000 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:01:00,007 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:01:00,008 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:01:00,008 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:01:00,008 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:01:00,008 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@41a0aa7d - End of configuration. [testng] 02:01:00,009 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6574a52c - Registering current configuration as safe fallback point [testng] 02:01:00,009 |-INFO in ch.qos.logback.classic.util.ContextInitializer@6c1a5b54 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 427 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-05 02:01:00,019] [main] java.version = 11.0.16 [testng] 02:01:00,023 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:01:00,023 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:01:00,069 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-05_02-01-00.log] [testng] 02:01:00,070 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-10-05 02:01:00,073] [main] testng.directory = /data [testng] [2024-10-05 02:01:00,073] [main] testng.configDirectory = /config [testng] [2024-10-05 02:01:00,328] [main] testng.multiplier = 1.0 [testng] [2024-10-05 02:01:00,329] [main] testng.in-memory = false [testng] [2024-10-05 02:01:00,329] [main] testng.allow-missing = false [testng] [2024-10-05 02:01:00,329] [main] user.language = en [testng] [2024-10-05 02:01:00,329] [main] user.country = ${user.country} [testng] [2024-10-05 02:01:00,330] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-05 02:01:05,579] [main] ---------------------------------------- [testng] [2024-10-05 02:01:05,579] [main] Total files: 76 [testng] [2024-10-05 02:01:05,579] [main] Scan time: 5.249 s (69 ms/file) [testng] [2024-10-05 02:01:05,579] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 73 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-05 02:03:43,138] [pool-1-thread-1] Initializing /data/qa-17305/image0_00021.tif: [testng] 02:03:43,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:03:43,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:03:43,141 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-05_02-03-43.log] [testng] 02:03:43,142 |-INFO in ch.qos.logback.core.sift.SiftProcessor@379aa166 - End of configuration. [testng] [2024-10-05 02:03:43,828] [pool-1-thread-12] Initializing /data/ciprian/fibroblast.tif: [testng] 02:03:43,828 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:03:43,828 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:03:43,830 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-05_02-03-43.log] [testng] 02:03:43,830 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6dc302c5 - End of configuration. [testng] [2024-10-05 02:03:45,091] [pool-1-thread-11] Initializing /data/arvonn/fura.cxd: [testng] 02:03:45,091 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:03:45,091 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:03:45,092 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-05_02-03-45.log] [testng] 02:03:45,093 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2053e1a8 - End of configuration. [testng] [2024-10-05 02:03:45,646] [pool-1-thread-10] Initializing /data/hopi/#2 2colors CFP0.36sgain1 YFP0.60sgain5.tif: [testng] 02:03:45,646 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:03:45,647 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:03:45,647 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-05_02-03-45.log] [testng] 02:03:45,648 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27e15a66 - End of configuration. [testng] [2024-10-05 02:03:47,204] [pool-1-thread-9] Initializing /data/hopi/#21 phase.tif: [testng] 02:03:47,204 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:03:47,204 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:03:47,205 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-05_02-03-47.log] [testng] 02:03:47,205 |-INFO in ch.qos.logback.core.sift.SiftProcessor@343274f1 - End of configuration. [testng] [2024-10-05 02:03:48,123] [pool-1-thread-8] Initializing /data/hopi/#1Hoechst 0.1s gain5.tif: [testng] 02:03:48,123 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:03:48,123 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:03:48,124 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-05_02-03-48.log] [testng] 02:03:48,124 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20a64566 - End of configuration. [testng] [2024-10-05 02:03:49,203] [pool-1-thread-7] Initializing /data/cecilia/CoreScope/Test_50_100.cxd: [testng] 02:03:49,203 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:03:49,203 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:03:49,204 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-05_02-03-49.log] [testng] 02:03:49,205 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17a39e06 - End of configuration. [testng] [2024-10-05 02:03:49,641] [pool-1-thread-6] Initializing /data/arvonn/gfpras2.avi: [testng] 02:03:49,642 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:03:49,642 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:03:49,642 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-05_02-03-49.log] [testng] 02:03:49,643 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67cbcf98 - End of configuration. [testng] [2024-10-05 02:03:49,879] [pool-1-thread-5] Initializing /data/alessandro/Data1_1.cxd: [testng] 02:03:49,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:03:49,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:03:49,880 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-05_02-03-49.log] [testng] 02:03:49,881 |-INFO in ch.qos.logback.core.sift.SiftProcessor@382061fc - End of configuration. [testng] [2024-10-05 02:03:50,256] [pool-1-thread-4] Initializing /data/martin/XYT-01.cxd: [testng] 02:03:50,256 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:03:50,256 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:03:50,257 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-05_02-03-50.log] [testng] 02:03:50,258 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f6c42e4 - End of configuration. [testng] [2024-10-05 02:03:50,623] [pool-1-thread-3] Initializing /data/martin/XY-01.tif: [testng] 02:03:50,623 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:03:50,623 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:03:50,624 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-05_02-03-50.log] [testng] 02:03:50,624 |-INFO in ch.qos.logback.core.sift.SiftProcessor@604c001f - End of configuration. [testng] [2024-10-05 02:03:51,701] [pool-1-thread-2] Initializing /data/arvonn/good pollen 2z.cxd: [testng] 02:03:51,701 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:03:51,701 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:03:51,702 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-05_02-03-51.log] [testng] 02:03:51,702 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8ac21fb - End of configuration. [testng] [2024-10-05 02:03:55,029] [pool-1-thread-6] Initializing /data/nico/b00.cxd: [testng] [2024-10-05 02:03:56,123] [pool-1-thread-4] Initializing /data/arvonn/Point Spread Function 02um Bead TRITC.cxd: [testng] [2024-10-05 02:03:57,107] [pool-1-thread-7] Initializing /data/martin/20090422bead20x_C1.ome.cxd: [testng] [2024-10-05 02:03:57,494] [pool-1-thread-2] Initializing /data/martin/Data1.cxd: [testng] [2024-10-05 02:03:58,029] [pool-1-thread-11] Initializing /data/hopi/#21 CFP filter.tif: [testng] [2024-10-05 02:03:58,772] [pool-1-thread-1] Initializing /data/jcb/BEAF and SuHw 0.25M NaCl 5-11-12 #2.cxd: [testng] [2024-10-05 02:03:59,265] [pool-1-thread-5] Initializing /data/martin/HCI sample files/XYZT test.cxd: [testng] [2024-10-05 02:03:59,839] [pool-1-thread-3] Initializing /data/jason/mb_220411PS.cxd: [testng] [2024-10-05 02:04:00,438] [pool-1-thread-8] Initializing /data/imagesc-72023/Data727.cxd: [testng] [2024-10-05 02:04:01,476] [pool-1-thread-9] Initializing /data/hopi/3 colors YFP(green)2.99s gain4 CFP(red) 0.48s gain4 and Hoechst(blue)0.96gain4.tif: [testng] [2024-10-05 02:04:02,433] [pool-1-thread-12] Initializing /data/cecilia/ts_05_13_10_5.cxd: [testng] [2024-10-05 02:04:02,742] [pool-1-thread-10] Initializing /data/arvonn/RG Z Beads.cxd: [testng] [2024-10-05 02:04:04,060] [pool-1-thread-6] Initializing /data/imagesc-90085/VASA_PC2FISH1.cxd: [testng] [2024-10-05 02:04:04,888] [pool-1-thread-4] Initializing /data/hopi/#21 two colors CFP(Red) YFP (green).tif: [testng] [2024-10-05 02:04:05,824] [pool-1-thread-2] Initializing /data/arvonn/gfpras_623.cxd: [testng] [2024-10-05 02:04:06,185] [pool-1-thread-7] Initializing /data/arvonn/shark.cxd: [testng] [2024-10-05 02:04:07,064] [pool-1-thread-12] Initializing /data/qa-11327/bone_tmp1981_00011.tif: [testng] [2024-10-05 02:04:07,702] [pool-1-thread-10] Initializing /data/martin/XY-03.tif: [testng] [2024-10-05 02:04:09,575] [pool-1-thread-1] Initializing /data/martin/HCI sample files/test_2.tif: [testng] [2024-10-05 02:04:11,215] [pool-1-thread-11] Initializing /data/martin/XYT-01.tif: [testng] [2024-10-05 02:04:12,223] [pool-1-thread-8] Initializing /data/martin/XY-ch-02.tif: [testng] [2024-10-05 02:04:13,193] [pool-1-thread-3] Initializing /data/martin/20090422bead20x_C2.ome.cxd: [testng] [2024-10-05 02:04:13,574] [pool-1-thread-5] Initializing /data/gh-3625/no_timestamp_for_real.cxd: [testng] [2024-10-05 02:04:14,341] [pool-1-thread-9] Initializing /data/nico/b00/Image3.tif: [testng] [2024-10-05 02:04:18,545] [pool-1-thread-6] Initializing /data/cecilia/CoreScope/Test_40_100.cxd: [testng] [2024-10-05 02:04:19,075] [pool-1-thread-2] Initializing /data/ciprian/Pollen Band.cxd: [testng] [2024-10-05 02:04:19,556] [pool-1-thread-7] Initializing /data/hopi/#2 phase.tif: [testng] [2024-10-05 02:04:22,624] [pool-1-thread-3] Initializing /data/cecilia/recheck_test2.cxd: [testng] [2024-10-05 02:04:24,267] [pool-1-thread-5] Initializing /data/nico/b00/Image2.tif: [testng] [2024-10-05 02:04:25,694] [pool-1-thread-12] Initializing /data/arvonn/Rat Fluor 2.cxd: [testng] [2024-10-05 02:04:26,279] [pool-1-thread-2] Initializing /data/ben/Data1.cxd: [testng] [2024-10-05 02:04:26,730] [pool-1-thread-6] Initializing /data/nico/b00/Image1.tif: [testng] [2024-10-05 02:04:27,422] [pool-1-thread-11] Initializing /data/nico/b00/Image4.tif: [testng] [2024-10-05 02:04:28,181] [pool-1-thread-4] Initializing /data/martin/XY-02.tif: [testng] [2024-10-05 02:04:29,060] [pool-1-thread-9] Initializing /data/imagesc-90085/Data00042.cxd: [testng] [2024-10-05 02:04:29,455] [pool-1-thread-1] Initializing /data/hopi/3 channel/#7 image#1F1-34 10min per f 2f per s green.avi: [testng] [2024-10-05 02:04:29,791] [pool-1-thread-10] Initializing /data/hopi/#1YFP 0.96s gain5.tif: [testng] [2024-10-05 02:04:31,929] [pool-1-thread-8] Initializing /data/nico/b00/Image6.tif: [testng] [2024-10-05 02:04:34,665] [pool-1-thread-3] Initializing /data/arvonn/New Particles from Imants.cxd: [testng] [2024-10-05 02:04:35,518] [pool-1-thread-1] Initializing /data/martin/HCI sample files/screenshot HCI.png: [testng] [2024-10-05 02:04:35,824] [pool-1-thread-7] Initializing /data/arvonn/gfpras2.cxd: [testng] [2024-10-05 02:04:36,355] [pool-1-thread-2] Initializing /data/hopi/3 channel/#7 image#1Rhod(r)0.48s gain5 YFP(g)0.36sgain2 CFP(blue)0.36sgain1cub1 every 10min.cxd: [testng] [2024-10-05 02:04:37,296] [pool-1-thread-9] Initializing /data/jcb/Test Run, 60 Sec PassesNEW.cxd: [testng] [2024-10-05 02:04:38,638] [pool-1-thread-5] Initializing /data/arvonn/3d Deconvolve Two Channel Sample.cxd: [testng] [2024-10-05 02:04:39,055] [pool-1-thread-12] Initializing /data/ciprian/Fura 2.cxd: [testng] [2024-10-05 02:04:39,775] [pool-1-thread-1] Initializing /data/jesper/1q35.cxd: [testng] [2024-10-05 02:04:40,885] [pool-1-thread-8] Initializing /data/arvonn/a rat 10x inverted qimaging 2 color 2000R-1.cxd: [testng] [2024-10-05 02:04:41,349] [pool-1-thread-6] Initializing /data/ascb/030811RPE1.1x100DICData2nebd.cxd: [testng] [2024-10-05 02:04:43,407] [pool-1-thread-11] Initializing /data/nico/b00/Image5.tif: [testng] [2024-10-05 02:04:45,486] [pool-1-thread-10] Initializing /data/qa-11073/tinCD4 GCamp5 tdTomato DualView #1 488 only6.cxd: [testng] [2024-10-05 02:04:46,769] [pool-1-thread-4] Initializing /data/nico/b00/Image8.tif: [testng] [2024-10-05 02:04:47,534] [pool-1-thread-3] Initializing /data/hopi/3 channel/#7 image#1F1-34 10min per f 2f per s.avi: [testng] [2024-10-05 02:04:47,741] [pool-1-thread-7] Initializing /data/georg/GCamp3xtinCD4, GCamp3_99wmn_01_BT.cxd: [testng] [2024-10-05 02:04:50,276] [pool-1-thread-12] Initializing /data/nico/b00/Image7.tif: [testng] [2024-10-05 02:04:51,784] [pool-1-thread-5] Initializing /data/hopi/#21 YFP filter.tif: [testng] [2024-10-05 02:04:52,810] [pool-1-thread-1] Initializing /data/hopi/time laps 10 min per frame YFP exposure 0.60s gain1 and CFP 0.36s gain1.cxd: [testng] [2024-10-05 02:04:53,505] [pool-1-thread-8] Initializing /data/martin/XY-ch-01.tif: [testng] [2024-10-05 02:04:54,902] [pool-1-thread-9] Initializing /data/martin/HCI sample files/XYT test 8x binning 286fps.cxd: [testng] [2024-10-05 02:04:55,404] [pool-1-thread-2] Initializing /data/ciprian/Maggot color.tif: [testng] [2024-10-05 02:04:56,576] [pool-1-thread-11] Initializing /data/ciprian/Color Pollen.cxd: [testng] [2024-10-05 02:04:57,684] [pool-1-thread-3] Initializing /data/martin/sample shift Mirella.cxd: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3869, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 4 minutes 16 seconds Finished: SUCCESS