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Started by upstream project "BIOFORMATS-test-repo" build number 59 originally caused by: Started by upstream project "Trigger" build number 66 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins7459759411491552416.sh + '[' simplepci = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_8727_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] 01:41:32,353 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:41:32,391 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:41:32,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:41:32,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:41:32,462 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:41:32,462 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:41:32,462 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:41:32,462 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:41:32,463 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@5c30a9b0 - End of configuration. [testng] 01:41:32,463 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@7a69b07 - Registering current configuration as safe fallback point [testng] 01:41:32,463 |-INFO in ch.qos.logback.classic.util.ContextInitializer@5e82df6a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 457 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-10 01:41:32,474] [main] java.version = 1.8.0_342 [testng] 01:41:32,477 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:41:32,478 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:32,603 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-10_01-41-32.log] [testng] 01:41:32,605 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-05-10 01:41:32,618] [main] testng.directory = /data [testng] [2024-05-10 01:41:32,618] [main] testng.configDirectory = /config [testng] [2024-05-10 01:41:32,665] [main] testng.multiplier = 1.0 [testng] [2024-05-10 01:41:32,666] [main] testng.in-memory = false [testng] [2024-05-10 01:41:32,666] [main] testng.allow-missing = false [testng] [2024-05-10 01:41:32,666] [main] user.language = en [testng] [2024-05-10 01:41:32,666] [main] user.country = ${user.country} [testng] [2024-05-10 01:41:32,666] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-05-10 01:41:34,186] [main] ---------------------------------------- [testng] [2024-05-10 01:41:34,187] [main] Total files: 76 [testng] [2024-05-10 01:41:34,187] [main] Scan time: 1.519 s (19 ms/file) [testng] [2024-05-10 01:41:34,187] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 73 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-10 01:43:29,170] [pool-1-thread-1] Initializing /data/ciprian/Maggot color.tif: [testng] 01:43:29,171 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:43:29,171 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:29,172 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-10_01-43-29.log] [testng] 01:43:29,172 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b82fcb6 - End of configuration. [testng] [2024-05-10 01:43:29,218] [pool-1-thread-12] Initializing /data/arvonn/fura.cxd: [testng] 01:43:29,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:43:29,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:29,220 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-10_01-43-29.log] [testng] 01:43:29,220 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f50bfea - End of configuration. [testng] [2024-05-10 01:43:29,297] [pool-1-thread-11] Initializing /data/nico/b00/Image5.tif: [testng] 01:43:29,298 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:43:29,298 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:29,299 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-10_01-43-29.log] [testng] 01:43:29,299 |-INFO in ch.qos.logback.core.sift.SiftProcessor@aea6427 - End of configuration. [testng] [2024-05-10 01:43:29,384] [pool-1-thread-10] Initializing /data/ben/Data1.cxd: [testng] 01:43:29,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:43:29,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:29,385 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-10_01-43-29.log] [testng] 01:43:29,386 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1831b830 - End of configuration. [testng] [2024-05-10 01:43:29,463] [pool-1-thread-9] Initializing /data/nico/b00/Image7.tif: [testng] 01:43:29,464 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:43:29,464 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:29,465 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-10_01-43-29.log] [testng] 01:43:29,465 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76a512ea - End of configuration. [testng] [2024-05-10 01:43:29,494] [pool-1-thread-8] Initializing /data/qa-11073/tinCD4 GCamp5 tdTomato DualView #1 488 only6.cxd: [testng] 01:43:29,494 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:43:29,494 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:29,495 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-10_01-43-29.log] [testng] 01:43:29,495 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2df49473 - End of configuration. [testng] [2024-05-10 01:43:30,115] [pool-1-thread-7] Initializing /data/arvonn/good pollen 2z.cxd: [testng] 01:43:30,115 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:43:30,115 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:30,116 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-10_01-43-30.log] [testng] 01:43:30,116 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4999265d - End of configuration. [testng] [2024-05-10 01:43:30,182] [pool-1-thread-6] Initializing /data/arvonn/shark.cxd: [testng] 01:43:30,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:43:30,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:30,183 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-10_01-43-30.log] [testng] 01:43:30,183 |-INFO in ch.qos.logback.core.sift.SiftProcessor@392f270 - End of configuration. [testng] [2024-05-10 01:43:30,255] [pool-1-thread-5] Initializing /data/arvonn/gfpras2.avi: [testng] 01:43:30,255 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:43:30,255 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:30,256 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-10_01-43-30.log] [testng] 01:43:30,257 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32b5cd2b - End of configuration. [testng] [2024-05-10 01:43:30,279] [pool-1-thread-4] Initializing /data/arvonn/gfpras2.cxd: [testng] 01:43:30,279 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:43:30,279 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:30,280 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-10_01-43-30.log] [testng] 01:43:30,280 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7782f36 - End of configuration. [testng] [2024-05-10 01:43:30,345] [pool-1-thread-3] Initializing /data/hopi/#21 YFP filter.tif: [testng] 01:43:30,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:43:30,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:30,346 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-10_01-43-30.log] [testng] 01:43:30,346 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13688d1d - End of configuration. [testng] [2024-05-10 01:43:30,385] [pool-1-thread-2] Initializing /data/imagesc-72023/Data727.cxd: [testng] 01:43:30,385 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:43:30,386 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:30,386 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-10_01-43-30.log] [testng] 01:43:30,386 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f860088 - End of configuration. [testng] [2024-05-10 01:43:31,940] [pool-1-thread-9] Initializing /data/nico/b00/Image8.tif: [testng] [2024-05-10 01:43:31,959] [pool-1-thread-11] Initializing /data/martin/XYT-01.cxd: [testng] [2024-05-10 01:43:31,989] [pool-1-thread-5] Initializing /data/ciprian/Color Pollen.cxd: [testng] [2024-05-10 01:43:32,017] [pool-1-thread-4] Initializing /data/nico/b00/Image6.tif: [testng] [2024-05-10 01:43:32,097] [pool-1-thread-1] Initializing /data/martin/XYT-01.tif: [testng] [2024-05-10 01:43:32,272] [pool-1-thread-6] Initializing /data/ciprian/fibroblast.tif: [testng] [2024-05-10 01:43:32,638] [pool-1-thread-12] Initializing /data/hopi/#21 phase.tif: [testng] [2024-05-10 01:43:32,849] [pool-1-thread-7] Initializing /data/martin/XY-03.tif: [testng] [2024-05-10 01:43:32,908] [pool-1-thread-10] Initializing /data/ascb/030811RPE1.1x100DICData2nebd.cxd: [testng] [2024-05-10 01:43:34,734] [pool-1-thread-2] Initializing /data/martin/20090422bead20x_C2.ome.cxd: [testng] [2024-05-10 01:43:34,795] [pool-1-thread-3] Initializing /data/arvonn/Rat Fluor 2.cxd: [testng] [2024-05-10 01:43:35,097] [pool-1-thread-9] Initializing /data/imagesc-90085/VASA_PC2FISH1.cxd: [testng] [2024-05-10 01:43:35,142] [pool-1-thread-4] Initializing /data/hopi/#2 phase.tif: [testng] [2024-05-10 01:43:35,217] [pool-1-thread-1] Initializing /data/martin/sample shift Mirella.cxd: [testng] [2024-05-10 01:43:35,296] [pool-1-thread-11] Initializing /data/martin/20090422bead20x_C1.ome.cxd: [testng] [2024-05-10 01:43:35,351] [pool-1-thread-5] Initializing /data/cecilia/recheck_test2.cxd: [testng] [2024-05-10 01:43:36,188] [pool-1-thread-6] Initializing /data/martin/HCI sample files/XYZT test.cxd: [testng] [2024-05-10 01:43:36,313] [pool-1-thread-5] Initializing /data/cecilia/ts_05_13_10_5.cxd: [testng] [2024-05-10 01:43:36,365] [pool-1-thread-2] Initializing /data/arvonn/a rat 10x inverted qimaging 2 color 2000R-1.cxd: [testng] [2024-05-10 01:43:36,563] [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] [2024-05-10 01:43:36,700] [pool-1-thread-12] Initializing /data/arvonn/gfpras_623.cxd: [testng] [2024-05-10 01:43:37,001] [pool-1-thread-4] Initializing /data/imagesc-90085/Data00042.cxd: [testng] [2024-05-10 01:43:37,090] [pool-1-thread-11] Initializing /data/nico/b00/Image2.tif: [testng] [2024-05-10 01:43:37,161] [pool-1-thread-1] Initializing /data/martin/HCI sample files/test_2.tif: [testng] [2024-05-10 01:43:37,306] [pool-1-thread-9] Initializing /data/qa-17305/image0_00021.tif: [testng] [2024-05-10 01:43:37,438] [pool-1-thread-5] Initializing /data/hopi/3 channel/#7 image#1F1-34 10min per f 2f per s green.avi: [testng] [2024-05-10 01:43:37,492] [pool-1-thread-11] Initializing /data/martin/XY-ch-02.tif: [testng] [2024-05-10 01:43:37,648] [pool-1-thread-2] Initializing /data/arvonn/3d Deconvolve Two Channel Sample.cxd: [testng] [2024-05-10 01:43:37,679] [pool-1-thread-12] Initializing /data/arvonn/Point Spread Function 02um Bead TRITC.cxd: [testng] [2024-05-10 01:43:37,806] [pool-1-thread-3] Initializing /data/hopi/#2 2colors CFP0.36sgain1 YFP0.60sgain5.tif: [testng] [2024-05-10 01:43:38,215] [pool-1-thread-6] Initializing /data/hopi/3 channel/#7 image#1Rhod(r)0.48s gain5 YFP(g)0.36sgain2 CFP(blue)0.36sgain1cub1 every 10min.cxd: [testng] [2024-05-10 01:43:38,404] [pool-1-thread-9] Initializing /data/hopi/#21 two colors CFP(Red) YFP (green).tif: [testng] [2024-05-10 01:43:38,456] [pool-1-thread-12] Initializing /data/jason/mb_220411PS.cxd: [testng] [2024-05-10 01:43:38,621] [pool-1-thread-5] Initializing /data/martin/XY-02.tif: [testng] [2024-05-10 01:43:38,749] [pool-1-thread-8] Initializing /data/gh-3625/no_timestamp_for_real.cxd: [testng] [2024-05-10 01:43:39,019] [pool-1-thread-4] Initializing /data/martin/HCI sample files/screenshot HCI.png: [testng] [2024-05-10 01:43:39,038] [pool-1-thread-1] Initializing /data/hopi/3 channel/#7 image#1F1-34 10min per f 2f per s.avi: [testng] [2024-05-10 01:43:39,068] [pool-1-thread-2] Initializing /data/nico/b00/Image4.tif: [testng] [2024-05-10 01:43:39,349] [pool-1-thread-2] Initializing /data/arvonn/RG Z Beads.cxd: [testng] [2024-05-10 01:43:39,430] [pool-1-thread-11] Initializing /data/martin/XY-ch-01.tif: [testng] [2024-05-10 01:43:39,530] [pool-1-thread-7] Initializing /data/jcb/Test Run, 60 Sec PassesNEW.cxd: [testng] [2024-05-10 01:43:39,643] [pool-1-thread-4] Initializing /data/martin/XY-01.tif: [testng] [2024-05-10 01:43:39,906] [pool-1-thread-3] Initializing /data/georg/GCamp3xtinCD4, GCamp3_99wmn_01_BT.cxd: [testng] [2024-05-10 01:43:40,969] [pool-1-thread-5] Initializing /data/hopi/#21 CFP filter.tif: [testng] [2024-05-10 01:43:41,203] [pool-1-thread-1] Initializing /data/nico/b00.cxd: [testng] [2024-05-10 01:43:41,273] [pool-1-thread-2] Initializing /data/ciprian/Fura 2.cxd: [testng] [2024-05-10 01:43:48,058] [pool-1-thread-9] Initializing /data/hopi/#1Hoechst 0.1s gain5.tif: [testng] [2024-05-10 01:43:48,175] [pool-1-thread-1] Initializing /data/martin/Data1.cxd: [testng] [2024-05-10 01:43:48,524] [pool-1-thread-12] Initializing /data/cecilia/CoreScope/Test_40_100.cxd: [testng] [2024-05-10 01:43:48,566] [pool-1-thread-4] Initializing /data/qa-11327/bone_tmp1981_00011.tif: [testng] [2024-05-10 01:43:48,711] [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] [2024-05-10 01:43:48,761] [pool-1-thread-6] Initializing /data/jesper/1q35.cxd: [testng] [2024-05-10 01:43:48,800] [pool-1-thread-11] Initializing /data/martin/HCI sample files/XYT test 8x binning 286fps.cxd: [testng] [2024-05-10 01:43:48,918] [pool-1-thread-5] Initializing /data/nico/b00/Image1.tif: [testng] [2024-05-10 01:43:48,969] [pool-1-thread-1] Initializing /data/ciprian/Pollen Band.cxd: [testng] [2024-05-10 01:43:49,284] [pool-1-thread-5] Initializing /data/hopi/#1YFP 0.96s gain5.tif: [testng] [2024-05-10 01:43:49,371] [pool-1-thread-8] Initializing /data/alessandro/Data1_1.cxd: [testng] [2024-05-10 01:43:49,511] [pool-1-thread-7] Initializing /data/cecilia/CoreScope/Test_50_100.cxd: [testng] [2024-05-10 01:43:49,543] [pool-1-thread-1] Initializing /data/jcb/BEAF and SuHw 0.25M NaCl 5-11-12 #2.cxd: [testng] [2024-05-10 01:43:49,637] [pool-1-thread-6] Initializing /data/arvonn/New Particles from Imants.cxd: [testng] [2024-05-10 01:43:49,859] [pool-1-thread-12] Initializing /data/nico/b00/Image3.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