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Started by upstream project "BIOFORMATS-test-repo" build number 207 originally caused by: Started by upstream project "Trigger" build number 233 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/jenkins13530360818215032830.sh + '[' simplepci = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_32842_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] 03:43:17,711 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:43:17,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:43:17,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:43:17,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:43:17,760 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:43:17,760 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:43:17,760 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:43:17,760 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:43:17,760 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@5e600dd5 - End of configuration. [testng] 03:43:17,761 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@a38c7fe - Registering current configuration as safe fallback point [testng] 03:43:17,761 |-INFO in ch.qos.logback.classic.util.ContextInitializer@6fdbe764 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 369 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-02 03:43:17,769] [main] java.version = 17.0.2 [testng] 03:43:17,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:43:17,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:43:17,835 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-02_03-43-17.log] [testng] 03:43:17,836 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-10-02 03:43:17,844] [main] testng.directory = /data [testng] [2024-10-02 03:43:17,845] [main] testng.configDirectory = /config [testng] [2024-10-02 03:43:17,855] [main] testng.multiplier = 1.0 [testng] [2024-10-02 03:43:17,856] [main] testng.in-memory = false [testng] [2024-10-02 03:43:17,856] [main] testng.allow-missing = false [testng] [2024-10-02 03:43:17,856] [main] user.language = en [testng] [2024-10-02 03:43:17,856] [main] user.country = ${user.country} [testng] [2024-10-02 03:43:17,856] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-02 03:43:47,642] [main] ---------------------------------------- [testng] [2024-10-02 03:43:47,642] [main] Total files: 76 [testng] [2024-10-02 03:43:47,642] [main] Scan time: 29.786 s (391 ms/file) [testng] [2024-10-02 03:43:47,643] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 73 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-02 03:54:15,419] [pool-1-thread-1] Initializing /data/ciprian/Fura 2.cxd: [testng] 03:54:15,419 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:54:15,419 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:54:15,420 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-02_03-54-15.log] [testng] 03:54:15,421 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f5b269d - End of configuration. [testng] [2024-10-02 03:54:17,477] [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] 03:54:17,477 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:54:17,477 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:54:17,478 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-02_03-54-17.log] [testng] 03:54:17,478 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30619282 - End of configuration. [testng] [2024-10-02 03:54:22,722] [pool-1-thread-11] Initializing /data/arvonn/3d Deconvolve Two Channel Sample.cxd: [testng] 03:54:22,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:54:22,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:54:22,723 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-02_03-54-22.log] [testng] 03:54:22,723 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f980cb2 - End of configuration. [testng] [2024-10-02 03:54:24,455] [pool-1-thread-10] Initializing /data/imagesc-90085/VASA_PC2FISH1.cxd: [testng] 03:54:24,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:54:24,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:54:24,456 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-02_03-54-24.log] [testng] 03:54:24,457 |-INFO in ch.qos.logback.core.sift.SiftProcessor@182bcf70 - End of configuration. [testng] [2024-10-02 03:54:25,724] [pool-1-thread-9] Initializing /data/hopi/3 channel/#7 image#1F1-34 10min per f 2f per s.avi: [testng] 03:54:25,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:54:25,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:54:25,725 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-02_03-54-25.log] [testng] 03:54:25,726 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62ad0087 - End of configuration. [testng] [2024-10-02 03:54:26,918] [pool-1-thread-8] Initializing /data/arvonn/Rat Fluor 2.cxd: [testng] 03:54:26,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:54:26,919 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:54:26,919 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-02_03-54-26.log] [testng] 03:54:26,920 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27eef18a - End of configuration. [testng] [2024-10-02 03:54:29,063] [pool-1-thread-7] Initializing /data/gh-3625/no_timestamp_for_real.cxd: [testng] 03:54:29,063 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:54:29,063 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:54:29,064 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-02_03-54-29.log] [testng] 03:54:29,065 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31029fc7 - End of configuration. [testng] [2024-10-02 03:54:30,189] [pool-1-thread-6] Initializing /data/cecilia/recheck_test2.cxd: [testng] 03:54:30,189 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:54:30,189 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:54:30,190 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-02_03-54-30.log] [testng] 03:54:30,190 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1333b22e - End of configuration. [testng] [2024-10-02 03:54:32,593] [pool-1-thread-5] Initializing /data/arvonn/gfpras2.cxd: [testng] 03:54:32,593 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:54:32,593 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:54:32,594 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-02_03-54-32.log] [testng] 03:54:32,595 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c1f9dc7 - End of configuration. [testng] [2024-10-02 03:54:33,718] [pool-1-thread-4] Initializing /data/nico/b00/Image7.tif: [testng] 03:54:33,718 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:54:33,718 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:54:33,719 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-02_03-54-33.log] [testng] 03:54:33,719 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ae80e56 - End of configuration. [testng] [2024-10-02 03:54:37,654] [pool-1-thread-3] Initializing /data/arvonn/New Particles from Imants.cxd: [testng] 03:54:37,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:54:37,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:54:37,655 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-02_03-54-37.log] [testng] 03:54:37,655 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79860d34 - End of configuration. [testng] [2024-10-02 03:54:39,336] [pool-1-thread-2] Initializing /data/nico/b00/Image2.tif: [testng] 03:54:39,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:54:39,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:54:39,336 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-02_03-54-39.log] [testng] 03:54:39,337 |-INFO in ch.qos.logback.core.sift.SiftProcessor@788e3003 - End of configuration. [testng] [2024-10-02 03:54:52,581] [pool-1-thread-9] Initializing /data/cecilia/CoreScope/Test_50_100.cxd: [testng] [2024-10-02 03:54:56,857] [pool-1-thread-5] Initializing /data/hopi/#21 phase.tif: [testng] [2024-10-02 03:55:01,945] [pool-1-thread-1] Initializing /data/martin/XY-03.tif: [testng] [2024-10-02 03:55:06,342] [pool-1-thread-6] Initializing /data/arvonn/shark.cxd: [testng] [2024-10-02 03:55:09,011] [pool-1-thread-3] Initializing /data/imagesc-72023/Data727.cxd: [testng] [2024-10-02 03:55:10,668] [pool-1-thread-11] Initializing /data/martin/HCI sample files/test_2.tif: [testng] [2024-10-02 03:55:14,461] [pool-1-thread-10] Initializing /data/martin/XY-ch-02.tif: [testng] [2024-10-02 03:55:19,908] [pool-1-thread-8] Initializing /data/arvonn/Point Spread Function 02um Bead TRITC.cxd: [testng] [2024-10-02 03:55:21,616] [pool-1-thread-7] Initializing /data/martin/XYT-01.tif: [testng] [2024-10-02 03:55:33,467] [pool-1-thread-9] Initializing /data/martin/HCI sample files/screenshot HCI.png: [testng] [2024-10-02 03:55:37,545] [pool-1-thread-2] Initializing /data/hopi/#1YFP 0.96s gain5.tif: [testng] [2024-10-02 03:55:42,527] [pool-1-thread-4] Initializing /data/martin/20090422bead20x_C1.ome.cxd: [testng] [2024-10-02 03:55:44,726] [pool-1-thread-8] Initializing /data/martin/HCI sample files/XYZT test.cxd: [testng] [2024-10-02 03:55:46,831] [pool-1-thread-6] Initializing /data/arvonn/RG Z Beads.cxd: [testng] [2024-10-02 03:55:48,384] [pool-1-thread-3] Initializing /data/ascb/030811RPE1.1x100DICData2nebd.cxd: [testng] [2024-10-02 03:55:51,176] [pool-1-thread-12] Initializing /data/martin/Data1.cxd: [testng] [2024-10-02 03:55:52,880] [pool-1-thread-9] Initializing /data/jason/mb_220411PS.cxd: [testng] [2024-10-02 03:55:57,794] [pool-1-thread-11] Initializing /data/ciprian/Color Pollen.cxd: [testng] [2024-10-02 03:56:05,933] [pool-1-thread-7] Initializing /data/ciprian/Maggot color.tif: [testng] [2024-10-02 03:56:09,973] [pool-1-thread-1] Initializing /data/nico/b00/Image4.tif: [testng] [2024-10-02 03:56:14,778] [pool-1-thread-10] Initializing /data/qa-17305/image0_00021.tif: [testng] [2024-10-02 03:56:19,418] [pool-1-thread-8] Initializing /data/nico/b00/Image6.tif: [testng] [2024-10-02 03:56:23,401] [pool-1-thread-12] Initializing /data/martin/XY-ch-01.tif: [testng] [2024-10-02 03:56:27,348] [pool-1-thread-6] Initializing /data/hopi/3 channel/#7 image#1F1-34 10min per f 2f per s green.avi: [testng] [2024-10-02 03:56:28,198] [pool-1-thread-4] Initializing /data/nico/b00/Image8.tif: [testng] [2024-10-02 03:56:32,323] [pool-1-thread-5] Initializing /data/nico/b00/Image1.tif: [testng] [2024-10-02 03:56:36,123] [pool-1-thread-3] Initializing /data/georg/GCamp3xtinCD4, GCamp3_99wmn_01_BT.cxd: [testng] [2024-10-02 03:56:38,585] [pool-1-thread-9] Initializing /data/hopi/#21 YFP filter.tif: [testng] [2024-10-02 03:56:44,659] [pool-1-thread-11] Initializing /data/hopi/time laps 10 min per frame YFP exposure 0.60s gain1 and CFP 0.36s gain1.cxd: [testng] [2024-10-02 03:56:47,002] [pool-1-thread-6] Initializing /data/hopi/#1Hoechst 0.1s gain5.tif: [testng] [2024-10-02 03:56:54,614] [pool-1-thread-2] Initializing /data/qa-11327/bone_tmp1981_00011.tif: [testng] [2024-10-02 03:57:02,613] [pool-1-thread-10] Initializing /data/ben/Data1.cxd: [testng] [2024-10-02 03:57:04,391] [pool-1-thread-8] Initializing /data/qa-11073/tinCD4 GCamp5 tdTomato DualView #1 488 only6.cxd: [testng] [2024-10-02 03:57:06,849] [pool-1-thread-3] Initializing /data/nico/b00/Image3.tif: [testng] [2024-10-02 03:57:11,126] [pool-1-thread-4] Initializing /data/martin/HCI sample files/XYT test 8x binning 286fps.cxd: [testng] [2024-10-02 03:57:12,454] [pool-1-thread-5] Initializing /data/ciprian/fibroblast.tif: [testng] [2024-10-02 03:57:17,147] [pool-1-thread-11] Initializing /data/arvonn/a rat 10x inverted qimaging 2 color 2000R-1.cxd: [testng] [2024-10-02 03:57:19,604] [pool-1-thread-1] Initializing /data/alessandro/Data1_1.cxd: [testng] [2024-10-02 03:57:21,484] [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] [2024-10-02 03:57:23,067] [pool-1-thread-7] Initializing /data/arvonn/gfpras2.avi: [testng] [2024-10-02 03:57:24,029] [pool-1-thread-9] Initializing /data/jcb/BEAF and SuHw 0.25M NaCl 5-11-12 #2.cxd: [testng] [2024-10-02 03:57:31,182] [pool-1-thread-7] Initializing /data/arvonn/good pollen 2z.cxd: [testng] [2024-10-02 03:57:33,091] [pool-1-thread-10] Initializing /data/martin/sample shift Mirella.cxd: [testng] [2024-10-02 03:57:39,668] [pool-1-thread-1] Initializing /data/cecilia/ts_05_13_10_5.cxd: [testng] [2024-10-02 03:57:41,665] [pool-1-thread-11] Initializing /data/jesper/1q35.cxd: [testng] [2024-10-02 03:57:43,803] [pool-1-thread-4] Initializing /data/hopi/#2 phase.tif: [testng] [2024-10-02 03:57:48,367] [pool-1-thread-2] Initializing /data/arvonn/gfpras_623.cxd: [testng] [2024-10-02 03:57:50,569] [pool-1-thread-6] Initializing /data/martin/XY-01.tif: [testng] [2024-10-02 03:57:55,122] [pool-1-thread-8] Initializing /data/martin/XY-02.tif: [testng] [2024-10-02 03:57:59,196] [pool-1-thread-9] Initializing /data/ciprian/Pollen Band.cxd: [testng] [2024-10-02 03:58:01,013] [pool-1-thread-12] Initializing /data/cecilia/CoreScope/Test_40_100.cxd: [testng] [2024-10-02 03:58:03,109] [pool-1-thread-3] Initializing /data/jcb/Test Run, 60 Sec PassesNEW.cxd: [testng] [2024-10-02 03:58:06,175] [pool-1-thread-5] Initializing /data/hopi/#21 two colors CFP(Red) YFP (green).tif: [testng] [2024-10-02 03:58:17,526] [pool-1-thread-10] Initializing /data/imagesc-90085/Data00042.cxd: [testng] [2024-10-02 03:58:19,465] [pool-1-thread-7] Initializing /data/martin/20090422bead20x_C2.ome.cxd: [testng] [2024-10-02 03:58:20,970] [pool-1-thread-1] Initializing /data/nico/b00/Image5.tif: [testng] [2024-10-02 03:58:25,827] [pool-1-thread-11] Initializing /data/hopi/#2 2colors CFP0.36sgain1 YFP0.60sgain5.tif: [testng] [2024-10-02 03:58:30,769] [pool-1-thread-2] Initializing /data/arvonn/fura.cxd: [testng] [2024-10-02 03:58:33,130] [pool-1-thread-9] Initializing /data/martin/XYT-01.cxd: [testng] [2024-10-02 03:58:40,638] [pool-1-thread-12] Initializing /data/hopi/#21 CFP filter.tif: [testng] [2024-10-02 03:58:44,890] [pool-1-thread-3] 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: 16 minutes 22 seconds Finished: SUCCESS