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Started by upstream project "BIOFORMATS-test-repo" build number 102 originally caused by: Started by upstream project "Trigger" build number 113 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins14282426606623247798.sh + '[' simplepci = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_15779_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 -Duser.language=fr -Duser.country=FR 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 test-automated: [testng] File leak detector installed [testng] 01:42:13,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:42:13,347 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:42:13,382 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:42:13,382 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:42:13,405 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:42:13,405 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:42:13,405 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:42:13,406 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:42:13,406 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@5c30a9b0 - End of configuration. [testng] 01:42:13,407 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@7a69b07 - Registering current configuration as safe fallback point [testng] 01:42:13,407 |-INFO in ch.qos.logback.classic.util.ContextInitializer@5e82df6a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 530 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-24 01:42:13,417] [main] java.version = 1.8.0_342 [testng] 01:42:13,421 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:42:13,421 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:42:13,558 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-24_01-42-13.log] [testng] 01:42:13,560 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-06-24 01:42:13,605] [main] testng.directory = /data [testng] [2024-06-24 01:42:13,605] [main] testng.configDirectory = /config [testng] [2024-06-24 01:42:13,738] [main] testng.multiplier = 1.0 [testng] [2024-06-24 01:42:13,739] [main] testng.in-memory = false [testng] [2024-06-24 01:42:13,739] [main] testng.allow-missing = false [testng] [2024-06-24 01:42:13,739] [main] user.language = fr [testng] [2024-06-24 01:42:13,739] [main] user.country = FR [testng] [2024-06-24 01:42:13,739] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-06-24 01:42:15,338] [main] ---------------------------------------- [testng] [2024-06-24 01:42:15,338] [main] Total files: 76 [testng] [2024-06-24 01:42:15,338] [main] Scan time: 1.599 s (21 ms/file) [testng] [2024-06-24 01:42:15,338] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 73 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-24 01:44:04,446] [pool-1-thread-1] Initializing /data/arvonn/good pollen 2z.cxd: [testng] 01:44:04,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:44:04,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:04,448 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-24_01-44-04.log] [testng] 01:44:04,448 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1db16fa6 - End of configuration. [testng] [2024-06-24 01:44:04,570] [pool-1-thread-12] Initializing /data/martin/XY-03.tif: [testng] 01:44:04,570 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:44:04,570 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:04,571 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-24_01-44-04.log] [testng] 01:44:04,571 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8757df5 - End of configuration. [testng] [2024-06-24 01:44:04,629] [pool-1-thread-11] Initializing /data/arvonn/RG Z Beads.cxd: [testng] 01:44:04,629 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:44:04,629 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:04,630 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-24_01-44-04.log] [testng] 01:44:04,630 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7117f072 - End of configuration. [testng] [2024-06-24 01:44:04,681] [pool-1-thread-10] Initializing /data/martin/XY-ch-02.tif: [testng] 01:44:04,681 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:44:04,681 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:04,682 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-24_01-44-04.log] [testng] 01:44:04,682 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b74bc18 - End of configuration. [testng] [2024-06-24 01:44:04,867] [pool-1-thread-9] Initializing /data/nico/b00/Image6.tif: [testng] 01:44:04,868 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:44:04,868 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:04,868 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-24_01-44-04.log] [testng] 01:44:04,869 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46eb95b5 - End of configuration. [testng] [2024-06-24 01:44:04,890] [pool-1-thread-8] Initializing /data/martin/sample shift Mirella.cxd: [testng] 01:44:04,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:44:04,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:04,891 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-24_01-44-04.log] [testng] 01:44:04,891 |-INFO in ch.qos.logback.core.sift.SiftProcessor@460d617d - End of configuration. [testng] [2024-06-24 01:44:04,950] [pool-1-thread-7] Initializing /data/nico/b00/Image3.tif: [testng] 01:44:04,951 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:44:04,951 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:04,951 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-24_01-44-04.log] [testng] 01:44:04,952 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a51697 - End of configuration. [testng] [2024-06-24 01:44:04,974] [pool-1-thread-6] Initializing /data/arvonn/3d Deconvolve Two Channel Sample.cxd: [testng] 01:44:04,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:44:04,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:04,975 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-24_01-44-04.log] [testng] 01:44:04,976 |-INFO in ch.qos.logback.core.sift.SiftProcessor@499080c3 - End of configuration. [testng] [2024-06-24 01:44:05,034] [pool-1-thread-5] Initializing /data/arvonn/New Particles from Imants.cxd: [testng] 01:44:05,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:44:05,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:05,035 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-24_01-44-05.log] [testng] 01:44:05,035 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ce45a53 - End of configuration. [testng] [2024-06-24 01:44:05,198] [pool-1-thread-4] Initializing /data/ciprian/Maggot color.tif: [testng] 01:44:05,198 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:44:05,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:05,199 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-24_01-44-05.log] [testng] 01:44:05,200 |-INFO in ch.qos.logback.core.sift.SiftProcessor@295265f6 - End of configuration. [testng] [2024-06-24 01:44:05,273] [pool-1-thread-3] Initializing /data/qa-17305/image0_00021.tif: [testng] 01:44:05,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:44:05,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:05,274 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-24_01-44-05.log] [testng] 01:44:05,274 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7da686f0 - End of configuration. [testng] [2024-06-24 01:44:05,324] [pool-1-thread-2] Initializing /data/hopi/#2 phase.tif: [testng] 01:44:05,325 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:44:05,325 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:05,325 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-24_01-44-05.log] [testng] 01:44:05,326 |-INFO in ch.qos.logback.core.sift.SiftProcessor@70605b81 - End of configuration. [testng] [2024-06-24 01:44:07,887] [pool-1-thread-7] Initializing /data/nico/b00/Image8.tif: [testng] [2024-06-24 01:44:07,919] [pool-1-thread-9] Initializing /data/ciprian/Pollen Band.cxd: [testng] [2024-06-24 01:44:07,943] [pool-1-thread-3] Initializing /data/nico/b00.cxd: [testng] [2024-06-24 01:44:07,960] [pool-1-thread-4] Initializing /data/ascb/030811RPE1.1x100DICData2nebd.cxd: [testng] [2024-06-24 01:44:09,180] [pool-1-thread-11] Initializing /data/qa-11327/bone_tmp1981_00011.tif: [testng] [2024-06-24 01:44:09,233] [pool-1-thread-6] Initializing /data/martin/HCI sample files/XYT test 8x binning 286fps.cxd: [testng] [2024-06-24 01:44:09,395] [pool-1-thread-1] Initializing /data/martin/Data1.cxd: [testng] [2024-06-24 01:44:09,425] [pool-1-thread-12] Initializing /data/arvonn/gfpras2.cxd: [testng] [2024-06-24 01:44:09,472] [pool-1-thread-8] Initializing /data/martin/XY-ch-01.tif: [testng] [2024-06-24 01:44:09,607] [pool-1-thread-2] Initializing /data/martin/XYT-01.cxd: [testng] [2024-06-24 01:44:09,813] [pool-1-thread-10] Initializing /data/jesper/1q35.cxd: [testng] [2024-06-24 01:44:09,846] [pool-1-thread-5] Initializing /data/nico/b00/Image4.tif: [testng] [2024-06-24 01:44:12,761] [pool-1-thread-3] Initializing /data/arvonn/Point Spread Function 02um Bead TRITC.cxd: [testng] [2024-06-24 01:44:12,882] [pool-1-thread-7] Initializing /data/hopi/3 colors YFP(green)2.99s gain4 CFP(red) 0.48s gain4 and Hoechst(blue)0.96gain4.tif: [testng] [2024-06-24 01:44:12,960] [pool-1-thread-5] Initializing /data/ciprian/Color Pollen.cxd: [testng] [2024-06-24 01:44:13,107] [pool-1-thread-9] Initializing /data/hopi/#21 YFP filter.tif: [testng] [2024-06-24 01:44:13,169] [pool-1-thread-2] Initializing /data/martin/HCI sample files/XYZT test.cxd: [testng] [2024-06-24 01:44:13,225] [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] [2024-06-24 01:44:13,398] [pool-1-thread-1] Initializing /data/arvonn/fura.cxd: [testng] [2024-06-24 01:44:13,515] [pool-1-thread-10] Initializing /data/imagesc-90085/Data00042.cxd: [testng] [2024-06-24 01:44:14,203] [pool-1-thread-5] Initializing /data/arvonn/gfpras2.avi: [testng] [2024-06-24 01:44:14,445] [pool-1-thread-3] Initializing /data/hopi/#2 2colors CFP0.36sgain1 YFP0.60sgain5.tif: [testng] [2024-06-24 01:44:14,727] [pool-1-thread-8] Initializing /data/alessandro/Data1_1.cxd: [testng] [2024-06-24 01:44:14,813] [pool-1-thread-1] Initializing /data/hopi/#21 CFP filter.tif: [testng] [2024-06-24 01:44:14,907] [pool-1-thread-6] Initializing /data/martin/HCI sample files/test_2.tif: [testng] [2024-06-24 01:44:15,056] [pool-1-thread-9] Initializing /data/jason/mb_220411PS.cxd: [testng] [2024-06-24 01:44:15,205] [pool-1-thread-5] Initializing /data/nico/b00/Image2.tif: [testng] [2024-06-24 01:44:15,386] [pool-1-thread-11] Initializing /data/georg/GCamp3xtinCD4, GCamp3_99wmn_01_BT.cxd: [testng] [2024-06-24 01:44:16,602] [pool-1-thread-8] Initializing /data/martin/20090422bead20x_C2.ome.cxd: [testng] [2024-06-24 01:44:16,677] [pool-1-thread-5] Initializing /data/cecilia/ts_05_13_10_5.cxd: [testng] [2024-06-24 01:44:16,721] [pool-1-thread-2] Initializing /data/hopi/#1Hoechst 0.1s gain5.tif: [testng] [2024-06-24 01:44:24,217] [pool-1-thread-10] Initializing /data/ciprian/fibroblast.tif: [testng] [2024-06-24 01:44:24,285] [pool-1-thread-7] Initializing /data/hopi/#21 phase.tif: [testng] [2024-06-24 01:44:24,646] [pool-1-thread-1] Initializing /data/jcb/Test Run, 60 Sec PassesNEW.cxd: [testng] [2024-06-24 01:44:24,904] [pool-1-thread-12] Initializing /data/cecilia/CoreScope/Test_40_100.cxd: [testng] [2024-06-24 01:44:25,036] [pool-1-thread-5] Initializing /data/imagesc-90085/VASA_PC2FISH1.cxd: [testng] [2024-06-24 01:44:25,209] [pool-1-thread-6] Initializing /data/gh-3625/no_timestamp_for_real.cxd: [testng] [2024-06-24 01:44:25,690] [pool-1-thread-8] Initializing /data/martin/XY-02.tif: [testng] [2024-06-24 01:44:25,751] [pool-1-thread-3] Initializing /data/martin/20090422bead20x_C1.ome.cxd: [testng] [2024-06-24 01:44:25,859] [pool-1-thread-7] Initializing /data/hopi/3 channel/#7 image#1F1-34 10min per f 2f per s green.avi: [testng] [2024-06-24 01:44:25,905] [pool-1-thread-10] Initializing /data/jcb/BEAF and SuHw 0.25M NaCl 5-11-12 #2.cxd: [testng] [2024-06-24 01:44:25,992] [pool-1-thread-2] Initializing /data/ben/Data1.cxd: [testng] [2024-06-24 01:44:26,354] [pool-1-thread-12] Initializing /data/ciprian/Fura 2.cxd: [testng] [2024-06-24 01:44:26,416] [pool-1-thread-9] Initializing /data/martin/XYT-01.tif: [testng] [2024-06-24 01:44:26,924] [pool-1-thread-9] Initializing /data/arvonn/gfpras_623.cxd: [testng] [2024-06-24 01:44:27,032] [pool-1-thread-8] Initializing /data/cecilia/CoreScope/Test_50_100.cxd: [testng] [2024-06-24 01:44:27,065] [pool-1-thread-12] Initializing /data/nico/b00/Image5.tif: [testng] [2024-06-24 01:44:27,136] [pool-1-thread-1] Initializing /data/qa-11073/tinCD4 GCamp5 tdTomato DualView #1 488 only6.cxd: [testng] [2024-06-24 01:44:27,987] [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] [2024-06-24 01:44:28,082] [pool-1-thread-2] Initializing /data/nico/b00/Image7.tif: [testng] [2024-06-24 01:44:28,192] [pool-1-thread-3] Initializing /data/arvonn/Rat Fluor 2.cxd: [testng] [2024-06-24 01:44:28,642] [pool-1-thread-12] Initializing /data/nico/b00/Image1.tif: [testng] [2024-06-24 01:44:28,663] [pool-1-thread-5] Initializing /data/hopi/#1YFP 0.96s gain5.tif: [testng] [2024-06-24 01:44:28,772] [pool-1-thread-9] Initializing /data/hopi/3 channel/#7 image#1F1-34 10min per f 2f per s.avi: [testng] [2024-06-24 01:44:28,820] [pool-1-thread-10] Initializing /data/imagesc-72023/Data727.cxd: [testng] [2024-06-24 01:44:28,907] [pool-1-thread-2] Initializing /data/martin/HCI sample files/screenshot HCI.png: [testng] [2024-06-24 01:44:29,156] [pool-1-thread-12] Initializing /data/arvonn/shark.cxd: [testng] [2024-06-24 01:44:29,223] [pool-1-thread-8] Initializing /data/cecilia/recheck_test2.cxd: [testng] [2024-06-24 01:44:29,666] [pool-1-thread-2] Initializing /data/arvonn/a rat 10x inverted qimaging 2 color 2000R-1.cxd: [testng] [2024-06-24 01:44:30,022] [pool-1-thread-8] Initializing /data/hopi/#21 two colors CFP(Red) YFP (green).tif: [testng] [2024-06-24 01:44:30,152] [pool-1-thread-6] Initializing /data/martin/XY-01.tif: [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 30 seconds Finished: SUCCESS