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Started by upstream project "BIOFORMATS-test-repo" build number 362 originally caused by: Started by upstream project "Trigger" build number 388 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/jenkins11182102981162030093.sh + '[' simplepci = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_57695_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] 01:04:55,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:04:55,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:04:55,204 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:04:55,204 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:04:55,210 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:04:55,210 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:04:55,210 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:04:55,211 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:04:55,211 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@242b836 - End of configuration. [testng] 01:04:55,211 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@534a5a98 - Registering current configuration as safe fallback point [testng] 01:04:55,211 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f80542f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 384 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-02 01:04:55,220] [main] java.version = 17.0.2 [testng] 01:04:55,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:04:55,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:04:55,385 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-02_01-04-55.log] [testng] 01:04:55,386 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration. [testng] [2025-03-02 01:04:55,388] [main] testng.directory = /data [testng] [2025-03-02 01:04:55,388] [main] testng.configDirectory = /config [testng] [2025-03-02 01:04:55,468] [main] testng.multiplier = 1.0 [testng] [2025-03-02 01:04:55,469] [main] testng.in-memory = false [testng] [2025-03-02 01:04:55,469] [main] testng.allow-missing = false [testng] [2025-03-02 01:04:55,469] [main] user.language = en [testng] [2025-03-02 01:04:55,469] [main] user.country = ${user.country} [testng] [2025-03-02 01:04:55,469] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-02 01:05:01,322] [main] ---------------------------------------- [testng] [2025-03-02 01:05:01,322] [main] Total files: 76 [testng] [2025-03-02 01:05:01,322] [main] Scan time: 5.853 s (77 ms/file) [testng] [2025-03-02 01:05:01,322] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 73 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-02 01:07:20,664] [pool-1-thread-1] Initializing /data/hopi/#1Hoechst 0.1s gain5.tif: [testng] 01:07:20,665 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:07:20,665 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:07:20,666 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-02_01-07-20.log] [testng] 01:07:20,666 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f5b269d - End of configuration. [testng] [2025-03-02 01:07:21,817] [pool-1-thread-12] Initializing /data/ciprian/Pollen Band.cxd: [testng] 01:07:21,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:07:21,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:07:21,819 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-02_01-07-21.log] [testng] 01:07:21,820 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d9ce27a - End of configuration. [testng] [2025-03-02 01:07:22,304] [pool-1-thread-11] Initializing /data/jcb/BEAF and SuHw 0.25M NaCl 5-11-12 #2.cxd: [testng] 01:07:22,305 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:07:22,305 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:07:22,305 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-02_01-07-22.log] [testng] 01:07:22,306 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a037373 - End of configuration. [testng] [2025-03-02 01:07:22,840] [pool-1-thread-10] Initializing /data/arvonn/fura.cxd: [testng] 01:07:22,841 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:07:22,841 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:07:22,841 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-02_01-07-22.log] [testng] 01:07:22,842 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37ff939c - End of configuration. [testng] [2025-03-02 01:07:23,359] [pool-1-thread-9] Initializing /data/martin/20090422bead20x_C2.ome.cxd: [testng] 01:07:23,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:07:23,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:07:23,360 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-02_01-07-23.log] [testng] 01:07:23,360 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f980cb2 - End of configuration. [testng] [2025-03-02 01:07:23,830] [pool-1-thread-8] Initializing /data/imagesc-90085/VASA_PC2FISH1.cxd: [testng] 01:07:23,830 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:07:23,830 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:07:23,831 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-02_01-07-23.log] [testng] 01:07:23,831 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fa04997 - End of configuration. [testng] [2025-03-02 01:07:24,323] [pool-1-thread-7] Initializing /data/arvonn/good pollen 2z.cxd: [testng] 01:07:24,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:07:24,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:07:24,324 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-02_01-07-24.log] [testng] 01:07:24,325 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58d4e50b - End of configuration. [testng] [2025-03-02 01:07:24,908] [pool-1-thread-6] Initializing /data/hopi/#21 YFP filter.tif: [testng] 01:07:24,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:07:24,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:07:24,909 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-02_01-07-24.log] [testng] 01:07:24,909 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31029fc7 - End of configuration. [testng] [2025-03-02 01:07:27,702] [pool-1-thread-5] Initializing /data/ciprian/fibroblast.tif: [testng] 01:07:27,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:07:27,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:07:27,703 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-02_01-07-27.log] [testng] 01:07:27,703 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c1f9dc7 - End of configuration. [testng] [2025-03-02 01:07:31,156] [pool-1-thread-4] Initializing /data/cecilia/CoreScope/Test_40_100.cxd: [testng] 01:07:31,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:07:31,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:07:31,157 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-02_01-07-31.log] [testng] 01:07:31,158 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ae80e56 - End of configuration. [testng] [2025-03-02 01:07:31,715] [pool-1-thread-3] Initializing /data/arvonn/gfpras2.avi: [testng] 01:07:31,715 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:07:31,715 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:07:31,716 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-02_01-07-31.log] [testng] 01:07:31,716 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79860d34 - End of configuration. [testng] [2025-03-02 01:07:32,051] [pool-1-thread-2] Initializing /data/nico/b00/Image8.tif: [testng] 01:07:32,052 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:07:32,052 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:07:32,052 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-02_01-07-32.log] [testng] 01:07:32,053 |-INFO in ch.qos.logback.core.sift.SiftProcessor@788e3003 - End of configuration. [testng] [2025-03-02 01:07:37,519] [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] [2025-03-02 01:07:38,905] [pool-1-thread-12] Initializing /data/cecilia/ts_05_13_10_5.cxd: [testng] [2025-03-02 01:07:39,502] [pool-1-thread-4] Initializing /data/nico/b00/Image1.tif: [testng] [2025-03-02 01:07:40,825] [pool-1-thread-7] Initializing /data/nico/b00/Image3.tif: [testng] [2025-03-02 01:07:41,986] [pool-1-thread-10] Initializing /data/jesper/1q35.cxd: [testng] [2025-03-02 01:07:42,540] [pool-1-thread-9] Initializing /data/arvonn/Point Spread Function 02um Bead TRITC.cxd: [testng] [2025-03-02 01:07:43,103] [pool-1-thread-11] Initializing /data/nico/b00/Image5.tif: [testng] [2025-03-02 01:07:44,343] [pool-1-thread-8] Initializing /data/martin/XYT-01.cxd: [testng] [2025-03-02 01:07:44,983] [pool-1-thread-2] Initializing /data/arvonn/gfpras2.cxd: [testng] [2025-03-02 01:07:50,003] [pool-1-thread-3] Initializing /data/martin/XY-ch-02.tif: [testng] [2025-03-02 01:07:51,561] [pool-1-thread-1] Initializing /data/hopi/#21 two colors CFP(Red) YFP (green).tif: [testng] [2025-03-02 01:07:52,750] [pool-1-thread-5] Initializing /data/martin/Data1.cxd: [testng] [2025-03-02 01:07:53,350] [pool-1-thread-6] Initializing /data/martin/XY-ch-01.tif: [testng] [2025-03-02 01:07:54,714] [pool-1-thread-9] Initializing /data/arvonn/gfpras_623.cxd: [testng] [2025-03-02 01:07:55,732] [pool-1-thread-12] Initializing /data/ciprian/Color Pollen.cxd: [testng] [2025-03-02 01:07:56,185] [pool-1-thread-8] Initializing /data/martin/XY-02.tif: [testng] [2025-03-02 01:07:57,272] [pool-1-thread-10] Initializing /data/martin/HCI sample files/test_2.tif: [testng] [2025-03-02 01:07:58,124] [pool-1-thread-2] Initializing /data/gh-3625/no_timestamp_for_real.cxd: [testng] [2025-03-02 01:07:59,846] [pool-1-thread-4] Initializing /data/hopi/#1YFP 0.96s gain5.tif: [testng] [2025-03-02 01:08:01,354] [pool-1-thread-11] Initializing /data/qa-11073/tinCD4 GCamp5 tdTomato DualView #1 488 only6.cxd: [testng] [2025-03-02 01:08:02,748] [pool-1-thread-7] Initializing /data/alessandro/Data1_1.cxd: [testng] [2025-03-02 01:08:05,311] [pool-1-thread-5] Initializing /data/nico/b00/Image7.tif: [testng] [2025-03-02 01:08:06,385] [pool-1-thread-9] Initializing /data/imagesc-90085/Data00042.cxd: [testng] [2025-03-02 01:08:06,947] [pool-1-thread-12] Initializing /data/nico/b00/Image2.tif: [testng] [2025-03-02 01:08:10,130] [pool-1-thread-7] Initializing /data/qa-17305/image0_00021.tif: [testng] [2025-03-02 01:08:10,879] [pool-1-thread-3] Initializing /data/hopi/#21 CFP filter.tif: [testng] [2025-03-02 01:08:12,262] [pool-1-thread-10] Initializing /data/hopi/3 colors YFP(green)2.99s gain4 CFP(red) 0.48s gain4 and Hoechst(blue)0.96gain4.tif: [testng] [2025-03-02 01:08:13,526] [pool-1-thread-2] Initializing /data/jcb/Test Run, 60 Sec PassesNEW.cxd: [testng] [2025-03-02 01:08:14,099] [pool-1-thread-8] Initializing /data/arvonn/a rat 10x inverted qimaging 2 color 2000R-1.cxd: [testng] [2025-03-02 01:08:15,354] [pool-1-thread-6] Initializing /data/ciprian/Fura 2.cxd: [testng] [2025-03-02 01:08:15,914] [pool-1-thread-1] Initializing /data/hopi/#21 phase.tif: [testng] [2025-03-02 01:08:16,828] [pool-1-thread-4] Initializing /data/arvonn/shark.cxd: [testng] [2025-03-02 01:08:17,493] [pool-1-thread-11] Initializing /data/hopi/#2 phase.tif: [testng] [2025-03-02 01:08:22,009] [pool-1-thread-9] Initializing /data/martin/XY-03.tif: [testng] [2025-03-02 01:08:25,136] [pool-1-thread-5] Initializing /data/nico/b00.cxd: [testng] [2025-03-02 01:08:25,766] [pool-1-thread-6] Initializing /data/ben/Data1.cxd: [testng] [2025-03-02 01:08:26,464] [pool-1-thread-12] Initializing /data/jason/mb_220411PS.cxd: [testng] [2025-03-02 01:08:27,085] [pool-1-thread-8] Initializing /data/martin/HCI sample files/XYT test 8x binning 286fps.cxd: [testng] [2025-03-02 01:08:27,630] [pool-1-thread-2] Initializing /data/arvonn/Rat Fluor 2.cxd: [testng] [2025-03-02 01:08:28,177] [pool-1-thread-7] Initializing /data/cecilia/recheck_test2.cxd: [testng] [2025-03-02 01:08:28,684] [pool-1-thread-4] Initializing /data/nico/b00/Image6.tif: [testng] [2025-03-02 01:08:33,983] [pool-1-thread-5] Initializing /data/georg/GCamp3xtinCD4, GCamp3_99wmn_01_BT.cxd: [testng] [2025-03-02 01:08:35,614] [pool-1-thread-6] Initializing /data/arvonn/3d Deconvolve Two Channel Sample.cxd: [testng] [2025-03-02 01:08:37,254] [pool-1-thread-3] Initializing /data/arvonn/New Particles from Imants.cxd: [testng] [2025-03-02 01:08:37,971] [pool-1-thread-10] Initializing /data/cecilia/CoreScope/Test_50_100.cxd: [testng] [2025-03-02 01:08:38,539] [pool-1-thread-1] Initializing /data/martin/XYT-01.tif: [testng] [2025-03-02 01:08:39,766] [pool-1-thread-11] Initializing /data/martin/HCI sample files/screenshot HCI.png: [testng] [2025-03-02 01:08:39,836] [pool-1-thread-7] Initializing /data/hopi/3 channel/#7 image#1F1-34 10min per f 2f per s.avi: [testng] [2025-03-02 01:08:40,547] [pool-1-thread-8] Initializing /data/martin/sample shift Mirella.cxd: [testng] [2025-03-02 01:08:41,088] [pool-1-thread-2] Initializing /data/ciprian/Maggot color.tif: [testng] [2025-03-02 01:08:42,615] [pool-1-thread-12] Initializing /data/hopi/#2 2colors CFP0.36sgain1 YFP0.60sgain5.tif: [testng] [2025-03-02 01:08:43,924] [pool-1-thread-9] Initializing /data/martin/HCI sample files/XYZT test.cxd: [testng] [2025-03-02 01:08:44,867] [pool-1-thread-4] Initializing /data/arvonn/RG Z Beads.cxd: [testng] [2025-03-02 01:08:45,729] [pool-1-thread-11] Initializing /data/imagesc-72023/Data727.cxd: [testng] [2025-03-02 01:08:48,098] [pool-1-thread-6] Initializing /data/martin/20090422bead20x_C1.ome.cxd: [testng] [2025-03-02 01:08:49,142] [pool-1-thread-7] Initializing /data/martin/XY-01.tif: [testng] [2025-03-02 01:08:50,619] [pool-1-thread-3] Initializing /data/qa-11327/bone_tmp1981_00011.tif: [testng] [2025-03-02 01:08:52,008] [pool-1-thread-10] Initializing /data/nico/b00/Image4.tif: [testng] [2025-03-02 01:08:53,587] [pool-1-thread-1] Initializing /data/ascb/030811RPE1.1x100DICData2nebd.cxd: [testng] [2025-03-02 01:08:55,341] [pool-1-thread-5] Initializing /data/hopi/3 channel/#7 image#1F1-34 10min per f 2f per s green.avi: [testng] [2025-03-02 01:08:56,010] [pool-1-thread-4] Initializing /data/hopi/3 channel/#7 image#1Rhod(r)0.48s gain5 YFP(g)0.36sgain2 CFP(blue)0.36sgain1cub1 every 10min.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 28 seconds Finished: SUCCESS