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Started by upstream project "BIOFORMATS-test-repo" build number 234 originally caused by: Started by upstream project "Trigger" build number 259 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins12702907321192369535.sh + '[' simplepci = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_36754_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 test-automated: [testng] File leak detector installed [testng] 02:26:16,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:26:16,398 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:26:16,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:26:16,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:26:16,447 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:26:16,447 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:26:16,447 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:26:16,448 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:26:16,448 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1139b2f3 - End of configuration. [testng] 02:26:16,449 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@3f197a46 - Registering current configuration as safe fallback point [testng] 02:26:16,449 |-INFO in ch.qos.logback.classic.util.ContextInitializer@636be97c - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 892 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-25 02:26:16,472] [main] java.version = 1.8.0_342 [testng] 02:26:16,476 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:26:16,476 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:26:16,555 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-25_02-26-16.log] [testng] 02:26:16,556 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-10-25 02:26:16,568] [main] testng.directory = /data [testng] [2024-10-25 02:26:16,568] [main] testng.configDirectory = /config [testng] [2024-10-25 02:26:16,586] [main] testng.multiplier = 1.0 [testng] [2024-10-25 02:26:16,587] [main] testng.in-memory = false [testng] [2024-10-25 02:26:16,587] [main] testng.allow-missing = false [testng] [2024-10-25 02:26:16,587] [main] user.language = en [testng] [2024-10-25 02:26:16,587] [main] user.country = ${user.country} [testng] [2024-10-25 02:26:16,587] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-25 02:26:21,748] [main] ---------------------------------------- [testng] [2024-10-25 02:26:21,749] [main] Total files: 76 [testng] [2024-10-25 02:26:21,749] [main] Scan time: 5.161 s (67 ms/file) [testng] [2024-10-25 02:26:21,749] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 73 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-25 02:28:21,303] [pool-1-thread-1] Initializing /data/alessandro/Data1_1.cxd: [testng] 02:28:21,303 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:28:21,303 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:21,304 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-25_02-28-21.log] [testng] 02:28:21,305 |-INFO in ch.qos.logback.core.sift.SiftProcessor@656948ac - End of configuration. [testng] [2024-10-25 02:28:21,564] [pool-1-thread-12] Initializing /data/jesper/1q35.cxd: [testng] 02:28:21,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:28:21,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:21,565 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-25_02-28-21.log] [testng] 02:28:21,565 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72bd9d7d - End of configuration. [testng] [2024-10-25 02:28:21,884] [pool-1-thread-11] Initializing /data/martin/20090422bead20x_C2.ome.cxd: [testng] 02:28:21,884 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:28:21,884 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:21,885 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-25_02-28-21.log] [testng] 02:28:21,886 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c36bef5 - End of configuration. [testng] [2024-10-25 02:28:22,294] [pool-1-thread-10] Initializing /data/martin/XY-ch-02.tif: [testng] 02:28:22,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:28:22,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:22,295 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-25_02-28-22.log] [testng] 02:28:22,296 |-INFO in ch.qos.logback.core.sift.SiftProcessor@746e35b - End of configuration. [testng] [2024-10-25 02:28:22,996] [pool-1-thread-9] Initializing /data/jcb/Test Run, 60 Sec PassesNEW.cxd: [testng] 02:28:22,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:28:22,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:22,997 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-25_02-28-22.log] [testng] 02:28:22,997 |-INFO in ch.qos.logback.core.sift.SiftProcessor@145feff9 - End of configuration. [testng] [2024-10-25 02:28:23,374] [pool-1-thread-8] Initializing /data/martin/20090422bead20x_C1.ome.cxd: [testng] 02:28:23,375 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:28:23,375 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:23,376 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-25_02-28-23.log] [testng] 02:28:23,376 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a378d67 - End of configuration. [testng] [2024-10-25 02:28:23,645] [pool-1-thread-7] Initializing /data/martin/XY-03.tif: [testng] 02:28:23,645 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:28:23,645 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:23,646 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-25_02-28-23.log] [testng] 02:28:23,646 |-INFO in ch.qos.logback.core.sift.SiftProcessor@301e9e2a - End of configuration. [testng] [2024-10-25 02:28:24,282] [pool-1-thread-6] Initializing /data/martin/HCI sample files/XYT test 8x binning 286fps.cxd: [testng] 02:28:24,282 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:28:24,282 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:24,283 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-25_02-28-24.log] [testng] 02:28:24,283 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ca80ad9 - End of configuration. [testng] [2024-10-25 02:28:24,669] [pool-1-thread-5] Initializing /data/martin/HCI sample files/test_2.tif: [testng] 02:28:24,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:28:24,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:24,671 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-25_02-28-24.log] [testng] 02:28:24,671 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c7b26fa - End of configuration. [testng] [2024-10-25 02:28:25,171] [pool-1-thread-4] Initializing /data/arvonn/gfpras_623.cxd: [testng] 02:28:25,172 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:28:25,172 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:25,172 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-25_02-28-25.log] [testng] 02:28:25,173 |-INFO in ch.qos.logback.core.sift.SiftProcessor@777607c - End of configuration. [testng] [2024-10-25 02:28:25,438] [pool-1-thread-3] Initializing /data/nico/b00/Image1.tif: [testng] 02:28:25,439 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:28:25,439 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:25,439 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-25_02-28-25.log] [testng] 02:28:25,440 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76b04db - End of configuration. [testng] [2024-10-25 02:28:26,028] [pool-1-thread-2] Initializing /data/cecilia/ts_05_13_10_5.cxd: [testng] 02:28:26,029 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:28:26,029 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:28:26,029 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-25_02-28-26.log] [testng] 02:28:26,029 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f70418c - End of configuration. [testng] [2024-10-25 02:28:29,864] [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] [2024-10-25 02:28:30,546] [pool-1-thread-12] Initializing /data/arvonn/good pollen 2z.cxd: [testng] [2024-10-25 02:28:30,894] [pool-1-thread-4] Initializing /data/nico/b00/Image7.tif: [testng] [2024-10-25 02:28:31,512] [pool-1-thread-1] Initializing /data/martin/XYT-01.cxd: [testng] [2024-10-25 02:28:31,776] [pool-1-thread-11] Initializing /data/arvonn/New Particles from Imants.cxd: [testng] [2024-10-25 02:28:32,233] [pool-1-thread-6] Initializing /data/martin/sample shift Mirella.cxd: [testng] [2024-10-25 02:28:32,498] [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] [2024-10-25 02:28:32,804] [pool-1-thread-9] Initializing /data/hopi/3 channel/#7 image#1F1-34 10min per f 2f per s green.avi: [testng] [2024-10-25 02:28:33,037] [pool-1-thread-3] Initializing /data/martin/XY-01.tif: [testng] [2024-10-25 02:28:33,860] [pool-1-thread-5] Initializing /data/hopi/#1Hoechst 0.1s gain5.tif: [testng] [2024-10-25 02:28:34,643] [pool-1-thread-7] Initializing /data/nico/b00.cxd: [testng] [2024-10-25 02:28:35,221] [pool-1-thread-10] Initializing /data/nico/b00/Image4.tif: [testng] [2024-10-25 02:28:37,142] [pool-1-thread-9] Initializing /data/arvonn/gfpras2.avi: [testng] [2024-10-25 02:28:37,354] [pool-1-thread-1] Initializing /data/ciprian/Fura 2.cxd: [testng] [2024-10-25 02:28:37,720] [pool-1-thread-7] Initializing /data/imagesc-72023/Data727.cxd: [testng] [2024-10-25 02:28:38,117] [pool-1-thread-12] Initializing /data/gh-3625/no_timestamp_for_real.cxd: [testng] [2024-10-25 02:28:38,620] [pool-1-thread-11] Initializing /data/cecilia/recheck_test2.cxd: [testng] [2024-10-25 02:28:38,913] [pool-1-thread-6] Initializing /data/hopi/#2 phase.tif: [testng] [2024-10-25 02:28:39,516] [pool-1-thread-8] Initializing /data/nico/b00/Image2.tif: [testng] [2024-10-25 02:28:40,416] [pool-1-thread-4] Initializing /data/ciprian/Color Pollen.cxd: [testng] [2024-10-25 02:28:40,800] [pool-1-thread-2] Initializing /data/imagesc-90085/VASA_PC2FISH1.cxd: [testng] [2024-10-25 02:28:41,208] [pool-1-thread-3] Initializing /data/nico/b00/Image3.tif: [testng] [2024-10-25 02:28:42,449] [pool-1-thread-9] Initializing /data/hopi/#21 YFP filter.tif: [testng] [2024-10-25 02:28:43,230] [pool-1-thread-10] Initializing /data/qa-17305/image0_00021.tif: [testng] [2024-10-25 02:28:44,351] [pool-1-thread-1] Initializing /data/martin/HCI sample files/screenshot HCI.png: [testng] [2024-10-25 02:28:44,448] [pool-1-thread-5] Initializing /data/ascb/030811RPE1.1x100DICData2nebd.cxd: [testng] [2024-10-25 02:28:46,686] [pool-1-thread-11] Initializing /data/nico/b00/Image6.tif: [testng] [2024-10-25 02:28:47,708] [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] [2024-10-25 02:28:48,193] [pool-1-thread-1] Initializing /data/arvonn/fura.cxd: [testng] [2024-10-25 02:28:49,570] [pool-1-thread-12] Initializing /data/ciprian/Maggot color.tif: [testng] [2024-10-25 02:28:50,543] [pool-1-thread-8] Initializing /data/arvonn/shark.cxd: [testng] [2024-10-25 02:28:50,969] [pool-1-thread-7] Initializing /data/cecilia/CoreScope/Test_40_100.cxd: [testng] [2024-10-25 02:28:51,744] [pool-1-thread-2] Initializing /data/hopi/#21 two colors CFP(Red) YFP (green).tif: [testng] [2024-10-25 02:28:52,774] [pool-1-thread-6] Initializing /data/nico/b00/Image5.tif: [testng] [2024-10-25 02:28:53,645] [pool-1-thread-3] Initializing /data/arvonn/RG Z Beads.cxd: [testng] [2024-10-25 02:28:54,438] [pool-1-thread-10] Initializing /data/hopi/#21 CFP filter.tif: [testng] [2024-10-25 02:28:56,355] [pool-1-thread-7] Initializing /data/qa-11073/tinCD4 GCamp5 tdTomato DualView #1 488 only6.cxd: [testng] [2024-10-25 02:28:57,216] [pool-1-thread-1] Initializing /data/ben/Data1.cxd: [testng] [2024-10-25 02:28:57,588] [pool-1-thread-8] Initializing /data/hopi/3 channel/#7 image#1F1-34 10min per f 2f per s.avi: [testng] [2024-10-25 02:28:57,756] [pool-1-thread-11] Initializing /data/jcb/BEAF and SuHw 0.25M NaCl 5-11-12 #2.cxd: [testng] [2024-10-25 02:28:58,260] [pool-1-thread-9] Initializing /data/ciprian/fibroblast.tif: [testng] [2024-10-25 02:28:59,002] [pool-1-thread-4] Initializing /data/hopi/#21 phase.tif: [testng] [2024-10-25 02:28:59,750] [pool-1-thread-3] Initializing /data/arvonn/Point Spread Function 02um Bead TRITC.cxd: [testng] [2024-10-25 02:29:00,159] [pool-1-thread-12] Initializing /data/arvonn/gfpras2.cxd: [testng] [2024-10-25 02:29:00,652] [pool-1-thread-5] Initializing /data/martin/Data1.cxd: [testng] [2024-10-25 02:29:01,126] [pool-1-thread-6] Initializing /data/arvonn/Rat Fluor 2.cxd: [testng] [2024-10-25 02:29:03,637] [pool-1-thread-1] Initializing /data/martin/XY-02.tif: [testng] [2024-10-25 02:29:04,206] [pool-1-thread-8] Initializing /data/martin/XYT-01.tif: [testng] [2024-10-25 02:29:04,840] [pool-1-thread-12] Initializing /data/hopi/#1YFP 0.96s gain5.tif: [testng] [2024-10-25 02:29:05,553] [pool-1-thread-3] Initializing /data/martin/XY-ch-01.tif: [testng] [2024-10-25 02:29:06,329] [pool-1-thread-5] Initializing /data/georg/GCamp3xtinCD4, GCamp3_99wmn_01_BT.cxd: [testng] [2024-10-25 02:29:07,595] [pool-1-thread-2] Initializing /data/cecilia/CoreScope/Test_50_100.cxd: [testng] [2024-10-25 02:29:07,816] [pool-1-thread-10] Initializing /data/martin/HCI sample files/XYZT test.cxd: [testng] [2024-10-25 02:29:08,382] [pool-1-thread-11] Initializing /data/hopi/#2 2colors CFP0.36sgain1 YFP0.60sgain5.tif: [testng] [2024-10-25 02:29:09,179] [pool-1-thread-4] Initializing /data/qa-11327/bone_tmp1981_00011.tif: [testng] [2024-10-25 02:29:09,801] [pool-1-thread-7] Initializing /data/nico/b00/Image8.tif: [testng] [2024-10-25 02:29:10,727] [pool-1-thread-6] Initializing /data/imagesc-90085/Data00042.cxd: [testng] [2024-10-25 02:29:11,063] [pool-1-thread-9] Initializing /data/arvonn/3d Deconvolve Two Channel Sample.cxd: [testng] [2024-10-25 02:29:13,004] [pool-1-thread-2] Initializing /data/arvonn/a rat 10x inverted qimaging 2 color 2000R-1.cxd: [testng] [2024-10-25 02:29:13,309] [pool-1-thread-8] Initializing /data/ciprian/Pollen Band.cxd: [testng] [2024-10-25 02:29:13,595] [pool-1-thread-1] Initializing /data/jason/mb_220411PS.cxd: [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 11 seconds Finished: SUCCESS