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Started by upstream project "BIOFORMATS-test-repo" build number 60 originally caused by: Started by upstream project "Trigger" build number 67 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins12840520230998963806.sh + '[' simplepci = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_8891_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] 01:41:46,425 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:41:46,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:41:46,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:41:46,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:41:46,502 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:41:46,503 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:41:46,503 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:41:46,503 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:41:46,503 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@41a0aa7d - End of configuration. [testng] 01:41:46,504 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6574a52c - Registering current configuration as safe fallback point [testng] 01:41:46,504 |-INFO in ch.qos.logback.classic.util.ContextInitializer@6c1a5b54 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 399 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-11 01:41:46,513] [main] java.version = 11.0.16 [testng] 01:41:46,517 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:41:46,517 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:46,613 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-11_01-41-46.log] [testng] 01:41:46,614 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-05-11 01:41:46,616] [main] testng.directory = /data [testng] [2024-05-11 01:41:46,617] [main] testng.configDirectory = /config [testng] [2024-05-11 01:41:46,628] [main] testng.multiplier = 1.0 [testng] [2024-05-11 01:41:46,629] [main] testng.in-memory = false [testng] [2024-05-11 01:41:46,629] [main] testng.allow-missing = false [testng] [2024-05-11 01:41:46,629] [main] user.language = en [testng] [2024-05-11 01:41:46,629] [main] user.country = ${user.country} [testng] [2024-05-11 01:41:46,629] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-05-11 01:41:48,158] [main] ---------------------------------------- [testng] [2024-05-11 01:41:48,158] [main] Total files: 76 [testng] [2024-05-11 01:41:48,159] [main] Scan time: 1.528 s (20 ms/file) [testng] [2024-05-11 01:41:48,159] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 73 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-11 01:43:37,052] [pool-1-thread-1] Initializing /data/ciprian/Fura 2.cxd: [testng] 01:43:37,053 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:43:37,053 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:37,055 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-11_01-43-37.log] [testng] 01:43:37,056 |-INFO in ch.qos.logback.core.sift.SiftProcessor@293f2f4b - End of configuration. [testng] [2024-05-11 01:43:37,120] [pool-1-thread-12] Initializing /data/hopi/3 colors YFP(green)2.99s gain4 CFP(red) 0.48s gain4 and Hoechst(blue)0.96gain4.tif: [testng] 01:43:37,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:43:37,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:37,121 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-11_01-43-37.log] [testng] 01:43:37,122 |-INFO in ch.qos.logback.core.sift.SiftProcessor@649a8dd4 - End of configuration. [testng] [2024-05-11 01:43:37,217] [pool-1-thread-11] Initializing /data/arvonn/3d Deconvolve Two Channel Sample.cxd: [testng] 01:43:37,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:43:37,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:37,218 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-11_01-43-37.log] [testng] 01:43:37,218 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7827d015 - End of configuration. [testng] [2024-05-11 01:43:37,435] [pool-1-thread-10] Initializing /data/imagesc-90085/VASA_PC2FISH1.cxd: [testng] 01:43:37,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:43:37,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:37,436 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-11_01-43-37.log] [testng] 01:43:37,436 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f50b196 - End of configuration. [testng] [2024-05-11 01:43:37,519] [pool-1-thread-9] Initializing /data/hopi/3 channel/#7 image#1F1-34 10min per f 2f per s.avi: [testng] 01:43:37,519 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:43:37,519 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:37,520 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-11_01-43-37.log] [testng] 01:43:37,520 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3030867e - End of configuration. [testng] [2024-05-11 01:43:37,557] [pool-1-thread-8] Initializing /data/arvonn/Rat Fluor 2.cxd: [testng] 01:43:37,557 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:43:37,557 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:37,558 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-11_01-43-37.log] [testng] 01:43:37,558 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8c2923b - End of configuration. [testng] [2024-05-11 01:43:37,960] [pool-1-thread-7] Initializing /data/gh-3625/no_timestamp_for_real.cxd: [testng] 01:43:37,960 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:43:37,960 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:37,961 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-11_01-43-37.log] [testng] 01:43:37,961 |-INFO in ch.qos.logback.core.sift.SiftProcessor@257d3f6c - End of configuration. [testng] [2024-05-11 01:43:38,157] [pool-1-thread-6] Initializing /data/cecilia/recheck_test2.cxd: [testng] 01:43:38,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:43:38,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:38,159 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-11_01-43-38.log] [testng] 01:43:38,159 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11cbf2cf - End of configuration. [testng] [2024-05-11 01:43:38,186] [pool-1-thread-5] Initializing /data/arvonn/gfpras2.cxd: [testng] 01:43:38,186 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:43:38,186 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:38,187 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-11_01-43-38.log] [testng] 01:43:38,187 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d366103 - End of configuration. [testng] [2024-05-11 01:43:38,208] [pool-1-thread-4] Initializing /data/nico/b00/Image7.tif: [testng] 01:43:38,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:43:38,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:38,209 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-11_01-43-38.log] [testng] 01:43:38,209 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2600ad43 - End of configuration. [testng] [2024-05-11 01:43:38,233] [pool-1-thread-3] Initializing /data/arvonn/New Particles from Imants.cxd: [testng] 01:43:38,234 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:43:38,234 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:38,235 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-11_01-43-38.log] [testng] 01:43:38,235 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3fed4755 - End of configuration. [testng] [2024-05-11 01:43:38,667] [pool-1-thread-2] Initializing /data/nico/b00/Image2.tif: [testng] 01:43:38,667 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:43:38,667 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:38,668 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-11_01-43-38.log] [testng] 01:43:38,668 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75aa29e0 - End of configuration. [testng] [2024-05-11 01:43:41,170] [pool-1-thread-2] Initializing /data/cecilia/CoreScope/Test_50_100.cxd: [testng] [2024-05-11 01:43:41,221] [pool-1-thread-4] Initializing /data/imagesc-72023/Data727.cxd: [testng] [2024-05-11 01:43:41,316] [pool-1-thread-1] Initializing /data/martin/XY-03.tif: [testng] [2024-05-11 01:43:41,370] [pool-1-thread-6] Initializing /data/arvonn/shark.cxd: [testng] [2024-05-11 01:43:41,464] [pool-1-thread-5] Initializing /data/hopi/#21 phase.tif: [testng] [2024-05-11 01:43:41,572] [pool-1-thread-9] Initializing /data/martin/XY-ch-02.tif: [testng] [2024-05-11 01:43:41,825] [pool-1-thread-11] Initializing /data/martin/HCI sample files/test_2.tif: [testng] [2024-05-11 01:43:42,043] [pool-1-thread-3] Initializing /data/martin/XYT-01.tif: [testng] [2024-05-11 01:43:42,645] [pool-1-thread-8] Initializing /data/arvonn/Point Spread Function 02um Bead TRITC.cxd: [testng] [2024-05-11 01:43:42,789] [pool-1-thread-10] Initializing /data/hopi/#1YFP 0.96s gain5.tif: [testng] [2024-05-11 01:43:42,877] [pool-1-thread-12] Initializing /data/martin/HCI sample files/screenshot HCI.png: [testng] [2024-05-11 01:43:43,178] [pool-1-thread-7] Initializing /data/martin/20090422bead20x_C1.ome.cxd: [testng] [2024-05-11 01:43:43,214] [pool-1-thread-2] Initializing /data/ascb/030811RPE1.1x100DICData2nebd.cxd: [testng] [2024-05-11 01:43:45,583] [pool-1-thread-6] Initializing /data/martin/Data1.cxd: [testng] [2024-05-11 01:43:45,696] [pool-1-thread-3] Initializing /data/arvonn/RG Z Beads.cxd: [testng] [2024-05-11 01:43:45,985] [pool-1-thread-1] Initializing /data/martin/HCI sample files/XYZT test.cxd: [testng] [2024-05-11 01:43:46,226] [pool-1-thread-5] Initializing /data/jason/mb_220411PS.cxd: [testng] [2024-05-11 01:43:46,404] [pool-1-thread-12] Initializing /data/ciprian/Color Pollen.cxd: [testng] [2024-05-11 01:43:46,592] [pool-1-thread-4] Initializing /data/ciprian/Maggot color.tif: [testng] [2024-05-11 01:43:46,739] [pool-1-thread-8] Initializing /data/nico/b00/Image4.tif: [testng] [2024-05-11 01:43:46,775] [pool-1-thread-9] Initializing /data/nico/b00/Image1.tif: [testng] [2024-05-11 01:43:46,910] [pool-1-thread-6] Initializing /data/nico/b00/Image8.tif: [testng] [2024-05-11 01:43:47,273] [pool-1-thread-3] Initializing /data/hopi/3 channel/#7 image#1F1-34 10min per f 2f per s green.avi: [testng] [2024-05-11 01:43:47,344] [pool-1-thread-10] Initializing /data/martin/XY-ch-01.tif: [testng] [2024-05-11 01:43:47,472] [pool-1-thread-9] Initializing /data/nico/b00/Image6.tif: [testng] [2024-05-11 01:43:47,492] [pool-1-thread-8] Initializing /data/georg/GCamp3xtinCD4, GCamp3_99wmn_01_BT.cxd: [testng] [2024-05-11 01:43:48,804] [pool-1-thread-11] Initializing /data/qa-17305/image0_00021.tif: [testng] [2024-05-11 01:43:48,916] [pool-1-thread-7] Initializing /data/hopi/time laps 10 min per frame YFP exposure 0.60s gain1 and CFP 0.36s gain1.cxd: [testng] [2024-05-11 01:43:49,031] [pool-1-thread-6] Initializing /data/hopi/#21 YFP filter.tif: [testng] [2024-05-11 01:43:49,108] [pool-1-thread-12] Initializing /data/hopi/#1Hoechst 0.1s gain5.tif: [testng] [2024-05-11 01:43:49,595] [pool-1-thread-9] Initializing /data/qa-11327/bone_tmp1981_00011.tif: [testng] [2024-05-11 01:43:49,653] [pool-1-thread-1] Initializing /data/ben/Data1.cxd: [testng] [2024-05-11 01:43:49,883] [pool-1-thread-4] Initializing /data/qa-11073/tinCD4 GCamp5 tdTomato DualView #1 488 only6.cxd: [testng] [2024-05-11 01:43:51,046] [pool-1-thread-11] Initializing /data/alessandro/Data1_1.cxd: [testng] [2024-05-11 01:43:51,154] [pool-1-thread-3] Initializing /data/arvonn/a rat 10x inverted qimaging 2 color 2000R-1.cxd: [testng] [2024-05-11 01:43:51,684] [pool-1-thread-5] Initializing /data/ciprian/fibroblast.tif: [testng] [2024-05-11 01:43:51,886] [pool-1-thread-1] Initializing /data/martin/HCI sample files/XYT test 8x binning 286fps.cxd: [testng] [2024-05-11 01:43:52,031] [pool-1-thread-6] Initializing /data/nico/b00/Image3.tif: [testng] [2024-05-11 01:43:52,281] [pool-1-thread-12] Initializing /data/arvonn/gfpras2.avi: [testng] [2024-05-11 01:43:52,641] [pool-1-thread-10] Initializing /data/hopi/3 channel/#7 image#1Rhod(r)0.48s gain5 YFP(g)0.36sgain2 CFP(blue)0.36sgain1cub1 every 10min.cxd: [testng] [2024-05-11 01:43:52,993] [pool-1-thread-3] Initializing /data/jcb/BEAF and SuHw 0.25M NaCl 5-11-12 #2.cxd: [testng] [2024-05-11 01:43:53,245] [pool-1-thread-6] Initializing /data/arvonn/good pollen 2z.cxd: [testng] [2024-05-11 01:43:53,386] [pool-1-thread-11] Initializing /data/martin/sample shift Mirella.cxd: [testng] [2024-05-11 01:43:53,471] [pool-1-thread-7] Initializing /data/cecilia/ts_05_13_10_5.cxd: [testng] [2024-05-11 01:43:53,761] [pool-1-thread-12] Initializing /data/jesper/1q35.cxd: [testng] [2024-05-11 01:43:54,103] [pool-1-thread-5] Initializing /data/martin/XY-01.tif: [testng] [2024-05-11 01:43:54,256] [pool-1-thread-1] Initializing /data/arvonn/gfpras_623.cxd: [testng] [2024-05-11 01:43:54,387] [pool-1-thread-9] Initializing /data/hopi/#2 phase.tif: [testng] [2024-05-11 01:43:54,510] [pool-1-thread-7] Initializing /data/martin/XY-02.tif: [testng] [2024-05-11 01:43:54,834] [pool-1-thread-12] Initializing /data/cecilia/CoreScope/Test_40_100.cxd: [testng] [2024-05-11 01:43:55,101] [pool-1-thread-6] Initializing /data/ciprian/Pollen Band.cxd: [testng] [2024-05-11 01:43:55,258] [pool-1-thread-11] Initializing /data/jcb/Test Run, 60 Sec PassesNEW.cxd: [testng] [2024-05-11 01:43:55,389] [pool-1-thread-1] Initializing /data/hopi/#21 two colors CFP(Red) YFP (green).tif: [testng] [2024-05-11 01:43:55,891] [pool-1-thread-3] Initializing /data/imagesc-90085/Data00042.cxd: [testng] [2024-05-11 01:43:56,087] [pool-1-thread-6] Initializing /data/martin/20090422bead20x_C2.ome.cxd: [testng] [2024-05-11 01:43:56,123] [pool-1-thread-12] Initializing /data/nico/b00/Image5.tif: [testng] [2024-05-11 01:43:56,155] [pool-1-thread-5] Initializing /data/martin/XYT-01.cxd: [testng] [2024-05-11 01:43:56,321] [pool-1-thread-9] Initializing /data/arvonn/fura.cxd: [testng] [2024-05-11 01:43:56,730] [pool-1-thread-7] Initializing /data/hopi/#2 2colors CFP0.36sgain1 YFP0.60sgain5.tif: [testng] [2024-05-11 01:43:56,930] [pool-1-thread-10] Initializing /data/hopi/#21 CFP filter.tif: [testng] [2024-05-11 01:43:57,048] [pool-1-thread-12] Initializing /data/nico/b00.cxd: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3869, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 2 minutes 25 seconds Finished: SUCCESS