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Started by upstream project "BIOFORMATS-test-repo" build number 80 originally caused by: Started by upstream project "Trigger" build number 88 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins12206888498247184115.sh + '[' simplepci = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_12171_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] 01:43:22,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:43:22,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:43:22,541 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:43:22,542 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:43:22,551 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:43:22,551 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:43:22,551 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:43:22,552 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:43:22,552 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@5c30a9b0 - End of configuration. [testng] 01:43:22,552 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@7a69b07 - Registering current configuration as safe fallback point [testng] 01:43:22,553 |-INFO in ch.qos.logback.classic.util.ContextInitializer@5e82df6a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 434 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-31 01:43:22,563] [main] java.version = 1.8.0_342 [testng] 01:43:22,566 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:43:22,566 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:43:22,612 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-31_01-43-22.log] [testng] 01:43:22,613 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-05-31 01:43:22,615] [main] testng.directory = /data [testng] [2024-05-31 01:43:22,616] [main] testng.configDirectory = /config [testng] [2024-05-31 01:43:22,633] [main] testng.multiplier = 1.0 [testng] [2024-05-31 01:43:22,634] [main] testng.in-memory = false [testng] [2024-05-31 01:43:22,634] [main] testng.allow-missing = false [testng] [2024-05-31 01:43:22,634] [main] user.language = en [testng] [2024-05-31 01:43:22,634] [main] user.country = ${user.country} [testng] [2024-05-31 01:43:22,634] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-05-31 01:43:24,070] [main] ---------------------------------------- [testng] [2024-05-31 01:43:24,070] [main] Total files: 76 [testng] [2024-05-31 01:43:24,070] [main] Scan time: 1.436 s (18 ms/file) [testng] [2024-05-31 01:43:24,070] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 73 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-31 01:45:16,397] [pool-1-thread-1] Initializing /data/ciprian/Maggot color.tif: [testng] 01:45:16,398 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:45:16,398 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:16,400 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-31_01-45-16.log] [testng] 01:45:16,401 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9790ff7 - End of configuration. [testng] [2024-05-31 01:45:16,490] [pool-1-thread-12] Initializing /data/arvonn/fura.cxd: [testng] 01:45:16,491 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:45:16,491 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:16,492 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-31_01-45-16.log] [testng] 01:45:16,492 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2117b111 - End of configuration. [testng] [2024-05-31 01:45:16,574] [pool-1-thread-11] Initializing /data/nico/b00/Image5.tif: [testng] 01:45:16,575 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:45:16,575 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:16,575 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-31_01-45-16.log] [testng] 01:45:16,576 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7572dc4a - End of configuration. [testng] [2024-05-31 01:45:16,609] [pool-1-thread-10] Initializing /data/ben/Data1.cxd: [testng] 01:45:16,609 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:45:16,609 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:16,610 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-31_01-45-16.log] [testng] 01:45:16,610 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a8bdac1 - End of configuration. [testng] [2024-05-31 01:45:16,718] [pool-1-thread-9] Initializing /data/nico/b00/Image7.tif: [testng] 01:45:16,718 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:45:16,718 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:16,719 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-31_01-45-16.log] [testng] 01:45:16,720 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47b6ac6c - End of configuration. [testng] [2024-05-31 01:45:16,747] [pool-1-thread-8] Initializing /data/qa-11073/tinCD4 GCamp5 tdTomato DualView #1 488 only6.cxd: [testng] 01:45:16,747 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:45:16,747 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:16,748 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-31_01-45-16.log] [testng] 01:45:16,748 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74fb282e - End of configuration. [testng] [2024-05-31 01:45:17,361] [pool-1-thread-7] Initializing /data/arvonn/good pollen 2z.cxd: [testng] 01:45:17,362 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:45:17,362 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:17,363 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-31_01-45-17.log] [testng] 01:45:17,363 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24af3973 - End of configuration. [testng] [2024-05-31 01:45:17,451] [pool-1-thread-6] Initializing /data/arvonn/shark.cxd: [testng] 01:45:17,452 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:45:17,452 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:17,452 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-31_01-45-17.log] [testng] 01:45:17,453 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d3468ef - End of configuration. [testng] [2024-05-31 01:45:17,569] [pool-1-thread-5] Initializing /data/arvonn/gfpras2.avi: [testng] 01:45:17,570 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:45:17,570 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:17,571 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-31_01-45-17.log] [testng] 01:45:17,572 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1fba6da3 - End of configuration. [testng] [2024-05-31 01:45:17,611] [pool-1-thread-4] Initializing /data/arvonn/gfpras2.cxd: [testng] 01:45:17,612 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:45:17,612 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:17,612 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-31_01-45-17.log] [testng] 01:45:17,613 |-INFO in ch.qos.logback.core.sift.SiftProcessor@159ede03 - End of configuration. [testng] [2024-05-31 01:45:17,647] [pool-1-thread-3] Initializing /data/hopi/#21 YFP filter.tif: [testng] 01:45:17,647 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:45:17,647 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:17,648 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-31_01-45-17.log] [testng] 01:45:17,648 |-INFO in ch.qos.logback.core.sift.SiftProcessor@526288c2 - End of configuration. [testng] [2024-05-31 01:45:17,714] [pool-1-thread-2] Initializing /data/imagesc-72023/Data727.cxd: [testng] 01:45:17,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:45:17,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:45:17,715 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-31_01-45-17.log] [testng] 01:45:17,715 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38813c - End of configuration. [testng] [2024-05-31 01:45:19,777] [pool-1-thread-9] Initializing /data/nico/b00/Image8.tif: [testng] [2024-05-31 01:45:19,842] [pool-1-thread-11] Initializing /data/martin/XYT-01.tif: [testng] [2024-05-31 01:45:19,869] [pool-1-thread-5] Initializing /data/martin/XYT-01.cxd: [testng] [2024-05-31 01:45:19,900] [pool-1-thread-4] Initializing /data/ciprian/Color Pollen.cxd: [testng] [2024-05-31 01:45:19,931] [pool-1-thread-1] Initializing /data/nico/b00/Image6.tif: [testng] [2024-05-31 01:45:19,952] [pool-1-thread-6] Initializing /data/ciprian/fibroblast.tif: [testng] [2024-05-31 01:45:20,036] [pool-1-thread-12] Initializing /data/hopi/#21 phase.tif: [testng] [2024-05-31 01:45:20,468] [pool-1-thread-10] Initializing /data/martin/XY-03.tif: [testng] [2024-05-31 01:45:20,630] [pool-1-thread-7] Initializing /data/ascb/030811RPE1.1x100DICData2nebd.cxd: [testng] [2024-05-31 01:45:21,983] [pool-1-thread-3] Initializing /data/martin/20090422bead20x_C2.ome.cxd: [testng] [2024-05-31 01:45:22,173] [pool-1-thread-1] Initializing /data/arvonn/Rat Fluor 2.cxd: [testng] [2024-05-31 01:45:22,388] [pool-1-thread-11] Initializing /data/imagesc-90085/VASA_PC2FISH1.cxd: [testng] [2024-05-31 01:45:22,435] [pool-1-thread-9] Initializing /data/hopi/#2 phase.tif: [testng] [2024-05-31 01:45:22,500] [pool-1-thread-2] Initializing /data/martin/sample shift Mirella.cxd: [testng] [2024-05-31 01:45:22,676] [pool-1-thread-5] Initializing /data/martin/20090422bead20x_C1.ome.cxd: [testng] [2024-05-31 01:45:22,760] [pool-1-thread-4] Initializing /data/cecilia/recheck_test2.cxd: [testng] [2024-05-31 01:45:23,493] [pool-1-thread-6] Initializing /data/martin/HCI sample files/XYZT test.cxd: [testng] [2024-05-31 01:45:23,719] [pool-1-thread-4] Initializing /data/cecilia/ts_05_13_10_5.cxd: [testng] [2024-05-31 01:45:23,855] [pool-1-thread-10] Initializing /data/arvonn/a rat 10x inverted qimaging 2 color 2000R-1.cxd: [testng] [2024-05-31 01:45:24,421] [pool-1-thread-12] Initializing /data/hopi/time laps 10 min per frame YFP exposure 0.60s gain1 and CFP 0.36s gain1.cxd: [testng] [2024-05-31 01:45:24,569] [pool-1-thread-3] Initializing /data/arvonn/gfpras_623.cxd: [testng] [2024-05-31 01:45:24,607] [pool-1-thread-5] Initializing /data/nico/b00/Image2.tif: [testng] [2024-05-31 01:45:24,625] [pool-1-thread-2] Initializing /data/imagesc-90085/Data00042.cxd: [testng] [2024-05-31 01:45:24,673] [pool-1-thread-9] Initializing /data/martin/HCI sample files/test_2.tif: [testng] [2024-05-31 01:45:24,755] [pool-1-thread-4] Initializing /data/qa-17305/image0_00021.tif: [testng] [2024-05-31 01:45:25,088] [pool-1-thread-5] Initializing /data/hopi/3 channel/#7 image#1F1-34 10min per f 2f per s green.avi: [testng] [2024-05-31 01:45:25,131] [pool-1-thread-10] Initializing /data/martin/XY-ch-02.tif: [testng] [2024-05-31 01:45:26,014] [pool-1-thread-11] Initializing /data/arvonn/3d Deconvolve Two Channel Sample.cxd: [testng] [2024-05-31 01:45:26,113] [pool-1-thread-3] Initializing /data/arvonn/Point Spread Function 02um Bead TRITC.cxd: [testng] [2024-05-31 01:45:26,392] [pool-1-thread-1] Initializing /data/hopi/#2 2colors CFP0.36sgain1 YFP0.60sgain5.tif: [testng] [2024-05-31 01:45:26,694] [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] [2024-05-31 01:45:27,034] [pool-1-thread-6] Initializing /data/hopi/#21 two colors CFP(Red) YFP (green).tif: [testng] [2024-05-31 01:45:27,435] [pool-1-thread-3] Initializing /data/jason/mb_220411PS.cxd: [testng] [2024-05-31 01:45:27,653] [pool-1-thread-5] Initializing /data/martin/XY-02.tif: [testng] [2024-05-31 01:45:27,787] [pool-1-thread-2] Initializing /data/gh-3625/no_timestamp_for_real.cxd: [testng] [2024-05-31 01:45:28,384] [pool-1-thread-11] Initializing /data/martin/HCI sample files/screenshot HCI.png: [testng] [2024-05-31 01:45:28,555] [pool-1-thread-9] Initializing /data/hopi/3 channel/#7 image#1F1-34 10min per f 2f per s.avi: [testng] [2024-05-31 01:45:28,929] [pool-1-thread-11] Initializing /data/nico/b00/Image4.tif: [testng] [2024-05-31 01:45:29,239] [pool-1-thread-10] Initializing /data/arvonn/RG Z Beads.cxd: [testng] [2024-05-31 01:45:29,318] [pool-1-thread-12] Initializing /data/martin/XY-ch-01.tif: [testng] [2024-05-31 01:45:29,596] [pool-1-thread-11] Initializing /data/jcb/Test Run, 60 Sec PassesNEW.cxd: [testng] [2024-05-31 01:45:30,016] [pool-1-thread-8] Initializing /data/martin/XY-01.tif: [testng] [2024-05-31 01:45:30,063] [pool-1-thread-5] Initializing /data/georg/GCamp3xtinCD4, GCamp3_99wmn_01_BT.cxd: [testng] [2024-05-31 01:45:31,497] [pool-1-thread-1] Initializing /data/hopi/#21 CFP filter.tif: [testng] [2024-05-31 01:45:31,564] [pool-1-thread-9] Initializing /data/nico/b00.cxd: [testng] [2024-05-31 01:45:31,582] [pool-1-thread-6] Initializing /data/ciprian/Fura 2.cxd: [testng] [2024-05-31 01:45:32,028] [pool-1-thread-9] Initializing /data/hopi/#1Hoechst 0.1s gain5.tif: [testng] [2024-05-31 01:45:32,238] [pool-1-thread-10] Initializing /data/martin/Data1.cxd: [testng] [2024-05-31 01:45:32,930] [pool-1-thread-4] Initializing /data/cecilia/CoreScope/Test_40_100.cxd: [testng] [2024-05-31 01:45:33,010] [pool-1-thread-6] Initializing /data/qa-11327/bone_tmp1981_00011.tif: [testng] [2024-05-31 01:45:33,229] [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] [2024-05-31 01:45:33,280] [pool-1-thread-8] Initializing /data/jesper/1q35.cxd: [testng] [2024-05-31 01:45:33,322] [pool-1-thread-3] Initializing /data/martin/HCI sample files/XYT test 8x binning 286fps.cxd: [testng] [2024-05-31 01:45:33,658] [pool-1-thread-10] Initializing /data/nico/b00/Image1.tif: [testng] [2024-05-31 01:45:33,918] [pool-1-thread-10] Initializing /data/ciprian/Pollen Band.cxd: [testng] [2024-05-31 01:45:33,993] [pool-1-thread-1] Initializing /data/hopi/#1YFP 0.96s gain5.tif: [testng] [2024-05-31 01:45:34,053] [pool-1-thread-11] Initializing /data/alessandro/Data1_1.cxd: [testng] [2024-05-31 01:45:34,146] [pool-1-thread-2] Initializing /data/cecilia/CoreScope/Test_50_100.cxd: [testng] [2024-05-31 01:45:34,228] [pool-1-thread-4] Initializing /data/jcb/BEAF and SuHw 0.25M NaCl 5-11-12 #2.cxd: [testng] [2024-05-31 01:45:35,253] [pool-1-thread-8] Initializing /data/arvonn/New Particles from Imants.cxd: [testng] [2024-05-31 01:45:35,638] [pool-1-thread-10] 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 25 seconds Finished: SUCCESS