Started by upstream project "BIOFORMATS-test-repo" build number 212 originally caused by: Started by upstream project "Trigger" build number 238 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/jenkins6585582814890102674.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_33662_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] 01:55:22,661 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:55:22,726 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:55:22,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:55:22,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:55:22,781 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:55:22,782 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:55:22,782 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:55:22,782 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:55:22,782 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@5c30a9b0 - End of configuration. [testng] 01:55:22,783 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@7a69b07 - Registering current configuration as safe fallback point [testng] 01:55:22,783 |-INFO in ch.qos.logback.classic.util.ContextInitializer@5e82df6a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 595 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-07 01:55:22,794] [main] java.version = 1.8.0_342 [testng] 01:55:22,798 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:55:22,798 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:55:22,848 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-07_01-55-22.log] [testng] 01:55:22,850 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-10-07 01:55:22,852] [main] testng.directory = /data [testng] [2024-10-07 01:55:22,852] [main] testng.configDirectory = /config [testng] [2024-10-07 01:55:22,869] [main] testng.multiplier = 1.0 [testng] [2024-10-07 01:55:22,869] [main] testng.in-memory = false [testng] [2024-10-07 01:55:22,869] [main] testng.allow-missing = false [testng] [2024-10-07 01:55:22,869] [main] user.language = fr [testng] [2024-10-07 01:55:22,869] [main] user.country = FR [testng] [2024-10-07 01:55:22,869] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-07 01:55:28,117] [main] ---------------------------------------- [testng] [2024-10-07 01:55:28,117] [main] Total files: 76 [testng] [2024-10-07 01:55:28,117] [main] Scan time: 5.248 s (69 ms/file) [testng] [2024-10-07 01:55:28,117] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 73 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-07 01:57:53,741] [pool-1-thread-1] Initializing /data/nico/b00/Image6.tif: [testng] 01:57:53,742 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:57:53,742 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:57:53,743 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-07_01-57-53.log] [testng] 01:57:53,744 |-INFO in ch.qos.logback.core.sift.SiftProcessor@348221ef - End of configuration. [testng] [2024-10-07 01:57:54,510] [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] 01:57:54,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:57:54,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:57:54,511 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-07_01-57-54.log] [testng] 01:57:54,512 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14961704 - End of configuration. [testng] [2024-10-07 01:57:55,151] [pool-1-thread-11] Initializing /data/imagesc-72023/Data727.cxd: [testng] 01:57:55,152 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:57:55,152 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:57:55,153 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-07_01-57-55.log] [testng] 01:57:55,154 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71c1cf6e - End of configuration. [testng] [2024-10-07 01:57:55,565] [pool-1-thread-10] Initializing /data/martin/HCI sample files/XYT test 8x binning 286fps.cxd: [testng] 01:57:55,565 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:57:55,565 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:57:55,566 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-07_01-57-55.log] [testng] 01:57:55,567 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3eef545 - End of configuration. [testng] [2024-10-07 01:57:56,033] [pool-1-thread-9] Initializing /data/hopi/3 channel/#7 image#1Rhod(r)0.48s gain5 YFP(g)0.36sgain2 CFP(blue)0.36sgain1cub1 every 10min.cxd: [testng] 01:57:56,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:57:56,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:57:56,034 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-07_01-57-56.log] [testng] 01:57:56,034 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1db6353b - End of configuration. [testng] [2024-10-07 01:57:56,533] [pool-1-thread-8] Initializing /data/hopi/time laps 10 min per frame YFP exposure 0.60s gain1 and CFP 0.36s gain1.cxd: [testng] 01:57:56,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:57:56,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:57:56,534 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-07_01-57-56.log] [testng] 01:57:56,535 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1152e126 - End of configuration. [testng] [2024-10-07 01:57:56,899] [pool-1-thread-7] Initializing /data/martin/20090422bead20x_C2.ome.cxd: [testng] 01:57:56,899 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:57:56,899 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:57:56,900 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-07_01-57-56.log] [testng] 01:57:56,900 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3606060f - End of configuration. [testng] [2024-10-07 01:57:57,213] [pool-1-thread-6] Initializing /data/imagesc-90085/VASA_PC2FISH1.cxd: [testng] 01:57:57,213 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:57:57,213 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:57:57,214 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-07_01-57-57.log] [testng] 01:57:57,214 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73191a74 - End of configuration. [testng] [2024-10-07 01:57:57,516] [pool-1-thread-5] Initializing /data/jcb/Test Run, 60 Sec PassesNEW.cxd: [testng] 01:57:57,517 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:57:57,517 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:57:57,517 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-07_01-57-57.log] [testng] 01:57:57,518 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68fad0d - End of configuration. [testng] [2024-10-07 01:57:57,924] [pool-1-thread-4] Initializing /data/arvonn/New Particles from Imants.cxd: [testng] 01:57:57,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:57:57,925 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:57:57,925 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-07_01-57-57.log] [testng] 01:57:57,925 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c474836 - End of configuration. [testng] [2024-10-07 01:57:58,262] [pool-1-thread-3] Initializing /data/martin/XY-01.tif: [testng] 01:57:58,262 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:57:58,262 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:57:58,263 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-07_01-57-58.log] [testng] 01:57:58,264 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3be4e27 - End of configuration. [testng] [2024-10-07 01:57:59,005] [pool-1-thread-2] Initializing /data/arvonn/gfpras_623.cxd: [testng] 01:57:59,005 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:57:59,005 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:57:59,007 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-07_01-57-59.log] [testng] 01:57:59,007 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6929c629 - End of configuration. [testng] [2024-10-07 01:58:03,302] [pool-1-thread-2] Initializing /data/hopi/#2 phase.tif: [testng] [2024-10-07 01:58:04,175] [pool-1-thread-7] Initializing /data/hopi/#21 CFP filter.tif: [testng] [2024-10-07 01:58:05,182] [pool-1-thread-4] Initializing /data/martin/HCI sample files/XYZT test.cxd: [testng] [2024-10-07 01:58:05,618] [pool-1-thread-5] Initializing /data/nico/b00.cxd: [testng] [2024-10-07 01:58:05,998] [pool-1-thread-6] Initializing /data/martin/HCI sample files/test_2.tif: [testng] [2024-10-07 01:58:06,744] [pool-1-thread-8] Initializing /data/jesper/1q35.cxd: [testng] [2024-10-07 01:58:07,185] [pool-1-thread-9] Initializing /data/hopi/#1Hoechst 0.1s gain5.tif: [testng] [2024-10-07 01:58:08,078] [pool-1-thread-11] Initializing /data/arvonn/Point Spread Function 02um Bead TRITC.cxd: [testng] [2024-10-07 01:58:08,505] [pool-1-thread-10] Initializing /data/martin/XYT-01.tif: [testng] [2024-10-07 01:58:09,275] [pool-1-thread-1] Initializing /data/nico/b00/Image7.tif: [testng] [2024-10-07 01:58:09,968] [pool-1-thread-3] Initializing /data/cecilia/ts_05_13_10_5.cxd: [testng] [2024-10-07 01:58:10,279] [pool-1-thread-12] Initializing /data/nico/b00/Image1.tif: [testng] [2024-10-07 01:58:13,562] [pool-1-thread-5] Initializing /data/martin/XY-ch-01.tif: [testng] [2024-10-07 01:58:14,662] [pool-1-thread-8] Initializing /data/qa-11073/tinCD4 GCamp5 tdTomato DualView #1 488 only6.cxd: [testng] [2024-10-07 01:58:15,683] [pool-1-thread-3] Initializing /data/arvonn/shark.cxd: [testng] [2024-10-07 01:58:16,080] [pool-1-thread-11] Initializing /data/alessandro/Data1_1.cxd: [testng] [2024-10-07 01:58:16,833] [pool-1-thread-4] Initializing /data/hopi/#21 YFP filter.tif: [testng] [2024-10-07 01:58:18,179] [pool-1-thread-1] Initializing /data/cecilia/recheck_test2.cxd: [testng] [2024-10-07 01:58:18,588] [pool-1-thread-10] Initializing /data/qa-11327/bone_tmp1981_00011.tif: [testng] [2024-10-07 01:58:19,362] [pool-1-thread-12] Initializing /data/ciprian/Maggot color.tif: [testng] [2024-10-07 01:58:20,898] [pool-1-thread-6] Initializing /data/arvonn/gfpras2.cxd: [testng] [2024-10-07 01:58:21,378] [pool-1-thread-2] Initializing /data/nico/b00/Image5.tif: [testng] [2024-10-07 01:58:22,270] [pool-1-thread-9] Initializing /data/arvonn/good pollen 2z.cxd: [testng] [2024-10-07 01:58:22,644] [pool-1-thread-7] Initializing /data/martin/XY-02.tif: [testng] [2024-10-07 01:58:23,541] [pool-1-thread-11] Initializing /data/martin/XY-03.tif: [testng] [2024-10-07 01:58:24,516] [pool-1-thread-5] Initializing /data/hopi/#21 two colors CFP(Red) YFP (green).tif: [testng] [2024-10-07 01:58:25,441] [pool-1-thread-3] Initializing /data/qa-17305/image0_00021.tif: [testng] [2024-10-07 01:58:27,494] [pool-1-thread-1] Initializing /data/ciprian/fibroblast.tif: [testng] [2024-10-07 01:58:28,418] [pool-1-thread-6] Initializing /data/nico/b00/Image4.tif: [testng] [2024-10-07 01:58:29,272] [pool-1-thread-8] Initializing /data/jcb/BEAF and SuHw 0.25M NaCl 5-11-12 #2.cxd: [testng] [2024-10-07 01:58:29,853] [pool-1-thread-12] Initializing /data/arvonn/Rat Fluor 2.cxd: [testng] [2024-10-07 01:58:30,529] [pool-1-thread-4] Initializing /data/martin/XYT-01.cxd: [testng] [2024-10-07 01:58:30,992] [pool-1-thread-9] Initializing /data/arvonn/fura.cxd: [testng] [2024-10-07 01:58:31,397] [pool-1-thread-2] Initializing /data/hopi/#2 2colors CFP0.36sgain1 YFP0.60sgain5.tif: [testng] [2024-10-07 01:58:33,501] [pool-1-thread-10] Initializing /data/arvonn/RG Z Beads.cxd: [testng] [2024-10-07 01:58:35,521] [pool-1-thread-3] Initializing /data/ascb/030811RPE1.1x100DICData2nebd.cxd: [testng] [2024-10-07 01:58:37,222] [pool-1-thread-7] Initializing /data/gh-3625/no_timestamp_for_real.cxd: [testng] [2024-10-07 01:58:38,052] [pool-1-thread-8] Initializing /data/martin/XY-ch-02.tif: [testng] [2024-10-07 01:58:39,063] [pool-1-thread-4] Initializing /data/arvonn/a rat 10x inverted qimaging 2 color 2000R-1.cxd: [testng] [2024-10-07 01:58:39,380] [pool-1-thread-9] Initializing /data/nico/b00/Image2.tif: [testng] [2024-10-07 01:58:40,209] [pool-1-thread-11] Initializing /data/ciprian/Pollen Band.cxd: [testng] [2024-10-07 01:58:40,582] [pool-1-thread-12] Initializing /data/georg/GCamp3xtinCD4, GCamp3_99wmn_01_BT.cxd: [testng] [2024-10-07 01:58:42,162] [pool-1-thread-5] Initializing /data/cecilia/CoreScope/Test_40_100.cxd: [testng] [2024-10-07 01:58:42,635] [pool-1-thread-6] Initializing /data/hopi/#1YFP 0.96s gain5.tif: [testng] [2024-10-07 01:58:43,560] [pool-1-thread-1] Initializing /data/hopi/3 channel/#7 image#1F1-34 10min per f 2f per s.avi: [testng] [2024-10-07 01:58:45,542] [pool-1-thread-10] Initializing /data/arvonn/3d Deconvolve Two Channel Sample.cxd: [testng] [2024-10-07 01:58:46,683] [pool-1-thread-11] Initializing /data/imagesc-90085/Data00042.cxd: [testng] [2024-10-07 01:58:53,336] [pool-1-thread-1] Initializing /data/nico/b00/Image8.tif: [testng] [2024-10-07 01:58:54,311] [pool-1-thread-2] Initializing /data/martin/20090422bead20x_C1.ome.cxd: [testng] [2024-10-07 01:58:54,842] [pool-1-thread-4] Initializing /data/ciprian/Color Pollen.cxd: [testng] [2024-10-07 01:58:55,279] [pool-1-thread-5] Initializing /data/martin/HCI sample files/screenshot HCI.png: [testng] [2024-10-07 01:58:56,053] [pool-1-thread-7] Initializing /data/martin/Data1.cxd: [testng] [2024-10-07 01:58:57,026] [pool-1-thread-5] Initializing /data/jason/mb_220411PS.cxd: [testng] [2024-10-07 01:58:57,951] [pool-1-thread-9] Initializing /data/arvonn/gfpras2.avi: [testng] [2024-10-07 01:58:58,331] [pool-1-thread-6] Initializing /data/cecilia/CoreScope/Test_50_100.cxd: [testng] [2024-10-07 01:58:58,787] [pool-1-thread-10] Initializing /data/ciprian/Fura 2.cxd: [testng] [2024-10-07 01:58:59,400] [pool-1-thread-11] Initializing /data/nico/b00/Image3.tif: [testng] [2024-10-07 01:59:00,589] [pool-1-thread-8] Initializing /data/martin/sample shift Mirella.cxd: [testng] [2024-10-07 01:59:02,213] [pool-1-thread-4] Initializing /data/hopi/#21 phase.tif: [testng] [2024-10-07 01:59:03,265] [pool-1-thread-9] Initializing /data/ben/Data1.cxd: [testng] [2024-10-07 01:59:03,914] [pool-1-thread-2] Initializing /data/hopi/3 channel/#7 image#1F1-34 10min per f 2f per s green.avi: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3869, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 3 minutes 54 seconds Finished: SUCCESS