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Started by upstream project "BIOFORMATS-test-repo" build number 269 originally caused by: Started by upstream project "Trigger" build number 292 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins14818727491210135481.sh + '[' simplepci = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_42494_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] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 01:24:08,074 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:24:08,111 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:24:08,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:24:08,135 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:24:08,144 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:24:08,144 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:24:08,144 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:24:08,145 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:24:08,145 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@5d534f5d - End of configuration. [testng] 01:24:08,146 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@51c668e3 - Registering current configuration as safe fallback point [testng] 01:24:08,146 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2e6a8155 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 425 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-27 01:24:08,160] [main] java.version = 17.0.2 [testng] 01:24:08,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:24:08,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:08,206 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-27_01-24-08.log] [testng] 01:24:08,207 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-11-27 01:24:08,210] [main] testng.directory = /data [testng] [2024-11-27 01:24:08,210] [main] testng.configDirectory = /config [testng] [2024-11-27 01:24:08,369] [main] testng.multiplier = 1.0 [testng] [2024-11-27 01:24:08,370] [main] testng.in-memory = false [testng] [2024-11-27 01:24:08,370] [main] testng.allow-missing = false [testng] [2024-11-27 01:24:08,370] [main] user.language = en [testng] [2024-11-27 01:24:08,370] [main] user.country = ${user.country} [testng] [2024-11-27 01:24:08,370] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-27 01:24:20,298] [main] ---------------------------------------- [testng] [2024-11-27 01:24:20,298] [main] Total files: 76 [testng] [2024-11-27 01:24:20,298] [main] Scan time: 11.928 s (156 ms/file) [testng] [2024-11-27 01:24:20,298] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 73 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-27 01:28:31,836] [pool-1-thread-1] Initializing /data/cecilia/ts_05_13_10_5.cxd: [testng] 01:28:31,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:28:31,837 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:31,838 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-27_01-28-31.log] [testng] 01:28:31,838 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1872a3db - End of configuration. [testng] [2024-11-27 01:28:32,904] [pool-1-thread-12] Initializing /data/ben/Data1.cxd: [testng] 01:28:32,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:28:32,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:32,905 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-27_01-28-32.log] [testng] 01:28:32,906 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f03aaa1 - End of configuration. [testng] [2024-11-27 01:28:33,873] [pool-1-thread-11] Initializing /data/hopi/3 channel/#7 image#1F1-34 10min per f 2f per s.avi: [testng] 01:28:33,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:28:33,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:33,875 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-27_01-28-33.log] [testng] 01:28:33,875 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f6b0032 - End of configuration. [testng] [2024-11-27 01:28:34,314] [pool-1-thread-10] Initializing /data/imagesc-72023/Data727.cxd: [testng] 01:28:34,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:28:34,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:34,315 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-27_01-28-34.log] [testng] 01:28:34,316 |-INFO in ch.qos.logback.core.sift.SiftProcessor@317547e1 - End of configuration. [testng] [2024-11-27 01:28:35,349] [pool-1-thread-9] Initializing /data/hopi/#21 two colors CFP(Red) YFP (green).tif: [testng] 01:28:35,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:28:35,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:35,350 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-27_01-28-35.log] [testng] 01:28:35,350 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d50d928 - End of configuration. [testng] [2024-11-27 01:28:37,735] [pool-1-thread-8] Initializing /data/arvonn/Point Spread Function 02um Bead TRITC.cxd: [testng] 01:28:37,735 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:28:37,735 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:37,736 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-27_01-28-37.log] [testng] 01:28:37,736 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5808b636 - End of configuration. [testng] [2024-11-27 01:28:38,585] [pool-1-thread-7] Initializing /data/ciprian/fibroblast.tif: [testng] 01:28:38,586 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:28:38,586 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:38,586 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-27_01-28-38.log] [testng] 01:28:38,587 |-INFO in ch.qos.logback.core.sift.SiftProcessor@317f7d1b - End of configuration. [testng] [2024-11-27 01:28:40,759] [pool-1-thread-6] Initializing /data/cecilia/CoreScope/Test_40_100.cxd: [testng] 01:28:40,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:28:40,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:40,760 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-27_01-28-40.log] [testng] 01:28:40,760 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a54c414 - End of configuration. [testng] [2024-11-27 01:28:41,720] [pool-1-thread-5] Initializing /data/arvonn/fura.cxd: [testng] 01:28:41,720 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:28:41,720 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:41,721 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-27_01-28-41.log] [testng] 01:28:41,721 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43428a11 - End of configuration. [testng] [2024-11-27 01:28:42,778] [pool-1-thread-4] Initializing /data/nico/b00/Image5.tif: [testng] 01:28:42,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:28:42,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:42,779 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-27_01-28-42.log] [testng] 01:28:42,780 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e8adef1 - End of configuration. [testng] [2024-11-27 01:28:45,052] [pool-1-thread-3] Initializing /data/alessandro/Data1_1.cxd: [testng] 01:28:45,052 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:28:45,052 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:45,053 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-27_01-28-45.log] [testng] 01:28:45,053 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d7500b2 - End of configuration. [testng] [2024-11-27 01:28:45,917] [pool-1-thread-2] Initializing /data/martin/sample shift Mirella.cxd: [testng] 01:28:45,917 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:28:45,917 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:45,917 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-27_01-28-45.log] [testng] 01:28:45,918 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61ff656d - End of configuration. [testng] [2024-11-27 01:28:54,449] [pool-1-thread-11] Initializing /data/hopi/#21 CFP filter.tif: [testng] [2024-11-27 01:28:58,539] [pool-1-thread-3] Initializing /data/arvonn/gfpras_623.cxd: [testng] [2024-11-27 01:28:59,608] [pool-1-thread-10] Initializing /data/martin/HCI sample files/XYT test 8x binning 286fps.cxd: [testng] [2024-11-27 01:29:00,807] [pool-1-thread-12] Initializing /data/arvonn/3d Deconvolve Two Channel Sample.cxd: [testng] [2024-11-27 01:29:01,836] [pool-1-thread-1] Initializing /data/martin/XY-ch-02.tif: [testng] [2024-11-27 01:29:04,291] [pool-1-thread-8] Initializing /data/martin/HCI sample files/XYZT test.cxd: [testng] [2024-11-27 01:29:05,474] [pool-1-thread-6] Initializing /data/martin/XY-03.tif: [testng] [2024-11-27 01:29:08,288] [pool-1-thread-2] Initializing /data/hopi/3 colors YFP(green)2.99s gain4 CFP(red) 0.48s gain4 and Hoechst(blue)0.96gain4.tif: [testng] [2024-11-27 01:29:11,422] [pool-1-thread-5] Initializing /data/martin/XY-01.tif: [testng] [2024-11-27 01:29:21,252] [pool-1-thread-4] Initializing /data/gh-3625/no_timestamp_for_real.cxd: [testng] [2024-11-27 01:29:22,773] [pool-1-thread-7] Initializing /data/jcb/Test Run, 60 Sec PassesNEW.cxd: [testng] [2024-11-27 01:29:25,808] [pool-1-thread-9] Initializing /data/martin/20090422bead20x_C1.ome.cxd: [testng] [2024-11-27 01:29:28,316] [pool-1-thread-3] Initializing /data/arvonn/good pollen 2z.cxd: [testng] [2024-11-27 01:29:29,382] [pool-1-thread-12] Initializing /data/arvonn/New Particles from Imants.cxd: [testng] [2024-11-27 01:29:30,534] [pool-1-thread-10] Initializing /data/martin/Data1.cxd: [testng] [2024-11-27 01:29:31,467] [pool-1-thread-8] Initializing /data/imagesc-90085/Data00042.cxd: [testng] [2024-11-27 01:29:34,611] [pool-1-thread-11] Initializing /data/cecilia/recheck_test2.cxd: [testng] [2024-11-27 01:29:38,215] [pool-1-thread-7] Initializing /data/ciprian/Color Pollen.cxd: [testng] [2024-11-27 01:29:39,451] [pool-1-thread-5] Initializing /data/nico/b00/Image2.tif: [testng] [2024-11-27 01:29:42,036] [pool-1-thread-4] Initializing /data/nico/b00/Image6.tif: [testng] [2024-11-27 01:29:44,473] [pool-1-thread-9] Initializing /data/martin/XYT-01.tif: [testng] [2024-11-27 01:29:47,553] [pool-1-thread-2] Initializing /data/nico/b00/Image4.tif: [testng] [2024-11-27 01:29:50,507] [pool-1-thread-6] Initializing /data/martin/XY-02.tif: [testng] [2024-11-27 01:29:53,332] [pool-1-thread-1] Initializing /data/hopi/#21 phase.tif: [testng] [2024-11-27 01:29:56,356] [pool-1-thread-10] Initializing /data/qa-11073/tinCD4 GCamp5 tdTomato DualView #1 488 only6.cxd: [testng] [2024-11-27 01:29:58,360] [pool-1-thread-8] Initializing /data/hopi/#2 phase.tif: [testng] [2024-11-27 01:30:01,654] [pool-1-thread-3] Initializing /data/ciprian/Pollen Band.cxd: [testng] [2024-11-27 01:30:04,537] [pool-1-thread-12] Initializing /data/hopi/3 channel/#7 image#1Rhod(r)0.48s gain5 YFP(g)0.36sgain2 CFP(blue)0.36sgain1cub1 every 10min.cxd: [testng] [2024-11-27 01:30:07,277] [pool-1-thread-11] Initializing /data/georg/GCamp3xtinCD4, GCamp3_99wmn_01_BT.cxd: [testng] [2024-11-27 01:30:09,945] [pool-1-thread-7] Initializing /data/nico/b00.cxd: [testng] [2024-11-27 01:30:14,913] [pool-1-thread-3] Initializing /data/arvonn/shark.cxd: [testng] [2024-11-27 01:30:19,513] [pool-1-thread-10] Initializing /data/nico/b00/Image8.tif: [testng] [2024-11-27 01:30:22,210] [pool-1-thread-4] Initializing /data/arvonn/RG Z Beads.cxd: [testng] [2024-11-27 01:30:23,301] [pool-1-thread-2] Initializing /data/arvonn/a rat 10x inverted qimaging 2 color 2000R-1.cxd: [testng] [2024-11-27 01:30:24,238] [pool-1-thread-12] Initializing /data/qa-11327/bone_tmp1981_00011.tif: [testng] [2024-11-27 01:30:26,956] [pool-1-thread-9] Initializing /data/nico/b00/Image1.tif: [testng] [2024-11-27 01:30:30,037] [pool-1-thread-5] Initializing /data/martin/20090422bead20x_C2.ome.cxd: [testng] [2024-11-27 01:30:31,376] [pool-1-thread-6] Initializing /data/ciprian/Maggot color.tif: [testng] [2024-11-27 01:30:34,296] [pool-1-thread-7] Initializing /data/hopi/3 channel/#7 image#1F1-34 10min per f 2f per s green.avi: [testng] [2024-11-27 01:30:36,057] [pool-1-thread-1] Initializing /data/imagesc-90085/VASA_PC2FISH1.cxd: [testng] [2024-11-27 01:30:37,434] [pool-1-thread-8] Initializing /data/arvonn/gfpras2.cxd: [testng] [2024-11-27 01:30:40,186] [pool-1-thread-3] Initializing /data/martin/XYT-01.cxd: [testng] [2024-11-27 01:30:41,938] [pool-1-thread-11] Initializing /data/cecilia/CoreScope/Test_50_100.cxd: [testng] [2024-11-27 01:30:43,683] [pool-1-thread-7] Initializing /data/jcb/BEAF and SuHw 0.25M NaCl 5-11-12 #2.cxd: [testng] [2024-11-27 01:30:47,474] [pool-1-thread-4] Initializing /data/martin/HCI sample files/screenshot HCI.png: [testng] [2024-11-27 01:30:47,565] [pool-1-thread-2] Initializing /data/hopi/#1YFP 0.96s gain5.tif: [testng] [2024-11-27 01:30:50,249] [pool-1-thread-5] Initializing /data/arvonn/gfpras2.avi: [testng] [2024-11-27 01:30:52,448] [pool-1-thread-8] Initializing /data/martin/HCI sample files/test_2.tif: [testng] [2024-11-27 01:30:54,729] [pool-1-thread-10] Initializing /data/ascb/030811RPE1.1x100DICData2nebd.cxd: [testng] [2024-11-27 01:30:57,425] [pool-1-thread-9] Initializing /data/qa-17305/image0_00021.tif: [testng] [2024-11-27 01:30:59,515] [pool-1-thread-6] Initializing /data/jason/mb_220411PS.cxd: [testng] [2024-11-27 01:31:00,617] [pool-1-thread-1] Initializing /data/ciprian/Fura 2.cxd: [testng] [2024-11-27 01:31:01,689] [pool-1-thread-3] Initializing /data/hopi/time laps 10 min per frame YFP exposure 0.60s gain1 and CFP 0.36s gain1.cxd: [testng] [2024-11-27 01:31:02,834] [pool-1-thread-12] Initializing /data/hopi/#21 YFP filter.tif: [testng] [2024-11-27 01:31:06,176] [pool-1-thread-11] Initializing /data/jesper/1q35.cxd: [testng] [2024-11-27 01:31:07,763] [pool-1-thread-4] Initializing /data/nico/b00/Image3.tif: [testng] [2024-11-27 01:31:12,882] [pool-1-thread-5] Initializing /data/martin/XY-ch-01.tif: [testng] [2024-11-27 01:31:17,091] [pool-1-thread-7] Initializing /data/arvonn/Rat Fluor 2.cxd: [testng] [2024-11-27 01:31:21,873] [pool-1-thread-1] Initializing /data/hopi/#1Hoechst 0.1s gain5.tif: [testng] [2024-11-27 01:31:24,653] [pool-1-thread-11] Initializing /data/hopi/#2 2colors CFP0.36sgain1 YFP0.60sgain5.tif: [testng] [2024-11-27 01:31:27,543] [pool-1-thread-3] Initializing /data/nico/b00/Image7.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3869, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 7 minutes 49 seconds Finished: SUCCESS