Started by upstream project "BIOFORMATS-test-repo" build number 227
originally caused by:
Started by upstream project "Trigger" build number 252
originally caused by:
Started by user devspace
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/jenkins9832809043034992071.sh
+ '[' simplepci = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_35605_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] 10:25:36,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 10:25:36,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 10:25:36,700 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 10:25:36,700 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 10:25:36,708 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 10:25:36,708 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 10:25:36,708 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 10:25:36,708 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 10:25:36,708 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1139b2f3 - End of configuration.
[testng] 10:25:36,709 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@3f197a46 - Registering current configuration as safe fallback point
[testng] 10:25:36,709 |-INFO in ch.qos.logback.classic.util.ContextInitializer@636be97c - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 396 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-10-18 10:25:36,719] [main] java.version = 1.8.0_342
[testng] 10:25:36,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 10:25:36,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:25:36,765 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-18_10-25-36.log]
[testng] 10:25:36,766 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration.
[testng] [2024-10-18 10:25:36,768] [main] testng.directory = /data
[testng] [2024-10-18 10:25:36,768] [main] testng.configDirectory = /config
[testng] [2024-10-18 10:25:36,780] [main] testng.multiplier = 1.0
[testng] [2024-10-18 10:25:36,780] [main] testng.in-memory = false
[testng] [2024-10-18 10:25:36,780] [main] testng.allow-missing = false
[testng] [2024-10-18 10:25:36,780] [main] user.language = en
[testng] [2024-10-18 10:25:36,780] [main] user.country = ${user.country}
[testng] [2024-10-18 10:25:36,780] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-10-18 10:25:42,294] [main] ----------------------------------------
[testng] [2024-10-18 10:25:42,294] [main] Total files: 76
[testng] [2024-10-18 10:25:42,295] [main] Scan time: 5.514 s (72 ms/file)
[testng] [2024-10-18 10:25:42,295] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 73 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-10-18 10:28:22,984] [pool-1-thread-1] Initializing /data/alessandro/Data1_1.cxd:
[testng] 10:28:22,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 10:28:22,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:28:22,986 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-18_10-28-22.log]
[testng] 10:28:22,986 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f7a2086 - End of configuration.
[testng] [2024-10-18 10:28:23,506] [pool-1-thread-12] Initializing /data/jesper/1q35.cxd:
[testng] 10:28:23,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 10:28:23,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:28:23,507 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-18_10-28-23.log]
[testng] 10:28:23,508 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23cfdabe - End of configuration.
[testng] [2024-10-18 10:28:23,997] [pool-1-thread-11] Initializing /data/martin/20090422bead20x_C2.ome.cxd:
[testng] 10:28:23,997 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 10:28:23,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:28:23,998 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-18_10-28-23.log]
[testng] 10:28:23,999 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c495897 - End of configuration.
[testng] [2024-10-18 10:28:24,499] [pool-1-thread-10] Initializing /data/martin/XY-ch-02.tif:
[testng] 10:28:24,500 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 10:28:24,500 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:28:24,500 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-18_10-28-24.log]
[testng] 10:28:24,501 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36d40569 - End of configuration.
[testng] [2024-10-18 10:28:25,770] [pool-1-thread-9] Initializing /data/jcb/Test Run, 60 Sec PassesNEW.cxd:
[testng] 10:28:25,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 10:28:25,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:28:25,771 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-18_10-28-25.log]
[testng] 10:28:25,771 |-INFO in ch.qos.logback.core.sift.SiftProcessor@138d689f - End of configuration.
[testng] [2024-10-18 10:28:26,332] [pool-1-thread-8] Initializing /data/martin/20090422bead20x_C1.ome.cxd:
[testng] 10:28:26,332 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 10:28:26,332 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:28:26,333 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-18_10-28-26.log]
[testng] 10:28:26,333 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c6d292f - End of configuration.
[testng] [2024-10-18 10:28:26,810] [pool-1-thread-7] Initializing /data/martin/XY-03.tif:
[testng] 10:28:26,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 10:28:26,810 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:28:26,811 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-18_10-28-26.log]
[testng] 10:28:26,811 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ca216d0 - End of configuration.
[testng] [2024-10-18 10:28:28,034] [pool-1-thread-6] Initializing /data/martin/HCI sample files/XYT test 8x binning 286fps.cxd:
[testng] 10:28:28,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 10:28:28,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:28:28,035 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-18_10-28-28.log]
[testng] 10:28:28,035 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7485d04f - End of configuration.
[testng] [2024-10-18 10:28:28,580] [pool-1-thread-5] Initializing /data/martin/HCI sample files/test_2.tif:
[testng] 10:28:28,580 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 10:28:28,580 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:28:28,581 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-18_10-28-28.log]
[testng] 10:28:28,581 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76866051 - End of configuration.
[testng] [2024-10-18 10:28:29,413] [pool-1-thread-4] Initializing /data/arvonn/gfpras_623.cxd:
[testng] 10:28:29,413 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 10:28:29,413 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:28:29,414 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-18_10-28-29.log]
[testng] 10:28:29,414 |-INFO in ch.qos.logback.core.sift.SiftProcessor@295e6498 - End of configuration.
[testng] [2024-10-18 10:28:29,889] [pool-1-thread-3] Initializing /data/nico/b00/Image1.tif:
[testng] 10:28:29,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 10:28:29,889 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:28:29,890 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-18_10-28-29.log]
[testng] 10:28:29,890 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d88a41f - End of configuration.
[testng] [2024-10-18 10:28:31,084] [pool-1-thread-2] Initializing /data/cecilia/ts_05_13_10_5.cxd:
[testng] 10:28:31,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 10:28:31,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 10:28:31,085 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-18_10-28-31.log]
[testng] 10:28:31,085 |-INFO in ch.qos.logback.core.sift.SiftProcessor@788311b6 - End of configuration.
[testng] [2024-10-18 10:28:36,420] [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] [2024-10-18 10:28:37,585] [pool-1-thread-6] Initializing /data/arvonn/good pollen 2z.cxd:
[testng] [2024-10-18 10:28:38,179] [pool-1-thread-12] Initializing /data/nico/b00/Image7.tif:
[testng] [2024-10-18 10:28:39,581] [pool-1-thread-4] Initializing /data/martin/XYT-01.cxd:
[testng] [2024-10-18 10:28:40,091] [pool-1-thread-1] Initializing /data/arvonn/New Particles from Imants.cxd:
[testng] [2024-10-18 10:28:40,740] [pool-1-thread-11] Initializing /data/martin/sample shift Mirella.cxd:
[testng] [2024-10-18 10:28:41,472] [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] [2024-10-18 10:28:42,312] [pool-1-thread-9] Initializing /data/hopi/3 channel/#7 image#1F1-34 10min per f 2f per s green.avi:
[testng] [2024-10-18 10:28:43,814] [pool-1-thread-5] Initializing /data/martin/XY-01.tif:
[testng] [2024-10-18 10:28:45,296] [pool-1-thread-7] Initializing /data/hopi/#1Hoechst 0.1s gain5.tif:
[testng] [2024-10-18 10:28:47,099] [pool-1-thread-3] Initializing /data/nico/b00.cxd:
[testng] [2024-10-18 10:28:47,864] [pool-1-thread-10] Initializing /data/nico/b00/Image4.tif:
[testng] [2024-10-18 10:28:51,042] [pool-1-thread-9] Initializing /data/arvonn/gfpras2.avi:
[testng] [2024-10-18 10:28:51,726] [pool-1-thread-4] Initializing /data/ciprian/Fura 2.cxd:
[testng] [2024-10-18 10:28:52,573] [pool-1-thread-11] Initializing /data/imagesc-72023/Data727.cxd:
[testng] [2024-10-18 10:28:53,266] [pool-1-thread-6] Initializing /data/gh-3625/no_timestamp_for_real.cxd:
[testng] [2024-10-18 10:28:54,348] [pool-1-thread-1] Initializing /data/hopi/#2 phase.tif:
[testng] [2024-10-18 10:28:56,124] [pool-1-thread-12] Initializing /data/cecilia/recheck_test2.cxd:
[testng] [2024-10-18 10:28:56,726] [pool-1-thread-3] Initializing /data/ciprian/Color Pollen.cxd:
[testng] [2024-10-18 10:28:57,221] [pool-1-thread-8] Initializing /data/nico/b00/Image2.tif:
[testng] [2024-10-18 10:28:58,429] [pool-1-thread-2] Initializing /data/nico/b00/Image3.tif:
[testng] [2024-10-18 10:28:59,977] [pool-1-thread-5] Initializing /data/imagesc-90085/VASA_PC2FISH1.cxd:
[testng] [2024-10-18 10:29:01,763] [pool-1-thread-9] Initializing /data/hopi/#21 YFP filter.tif:
[testng] [2024-10-18 10:29:03,211] [pool-1-thread-10] Initializing /data/qa-17305/image0_00021.tif:
[testng] [2024-10-18 10:29:05,118] [pool-1-thread-12] Initializing /data/martin/HCI sample files/screenshot HCI.png:
[testng] [2024-10-18 10:29:05,168] [pool-1-thread-3] Initializing /data/nico/b00/Image6.tif:
[testng] [2024-10-18 10:29:06,505] [pool-1-thread-4] Initializing /data/ascb/030811RPE1.1x100DICData2nebd.cxd:
[testng] [2024-10-18 10:29:09,796] [pool-1-thread-11] Initializing /data/hopi/3 channel/#7 image#1Rhod(r)0.48s gain5 YFP(g)0.36sgain2 CFP(blue)0.36sgain1cub1 every 10min.cxd:
[testng] [2024-10-18 10:29:10,733] [pool-1-thread-7] Initializing /data/arvonn/fura.cxd:
[testng] [2024-10-18 10:29:11,528] [pool-1-thread-6] Initializing /data/cecilia/CoreScope/Test_40_100.cxd:
[testng] [2024-10-18 10:29:12,377] [pool-1-thread-8] Initializing /data/arvonn/shark.cxd:
[testng] [2024-10-18 10:29:13,183] [pool-1-thread-5] Initializing /data/ciprian/Maggot color.tif:
[testng] [2024-10-18 10:29:15,394] [pool-1-thread-1] Initializing /data/hopi/#21 two colors CFP(Red) YFP (green).tif:
[testng] [2024-10-18 10:29:17,410] [pool-1-thread-12] Initializing /data/nico/b00/Image5.tif:
[testng] [2024-10-18 10:29:19,123] [pool-1-thread-2] Initializing /data/arvonn/RG Z Beads.cxd:
[testng] [2024-10-18 10:29:20,661] [pool-1-thread-10] Initializing /data/hopi/#21 CFP filter.tif:
[testng] [2024-10-18 10:29:22,858] [pool-1-thread-6] Initializing /data/qa-11073/tinCD4 GCamp5 tdTomato DualView #1 488 only6.cxd:
[testng] [2024-10-18 10:29:23,971] [pool-1-thread-8] Initializing /data/ben/Data1.cxd:
[testng] [2024-10-18 10:29:24,721] [pool-1-thread-9] Initializing /data/ciprian/fibroblast.tif:
[testng] [2024-10-18 10:29:26,358] [pool-1-thread-7] Initializing /data/hopi/3 channel/#7 image#1F1-34 10min per f 2f per s.avi:
[testng] [2024-10-18 10:29:26,698] [pool-1-thread-3] Initializing /data/jcb/BEAF and SuHw 0.25M NaCl 5-11-12 #2.cxd:
[testng] [2024-10-18 10:29:27,365] [pool-1-thread-11] Initializing /data/hopi/#21 phase.tif:
[testng] [2024-10-18 10:29:29,199] [pool-1-thread-4] Initializing /data/arvonn/Point Spread Function 02um Bead TRITC.cxd:
[testng] [2024-10-18 10:29:29,947] [pool-1-thread-5] Initializing /data/arvonn/gfpras2.cxd:
[testng] [2024-10-18 10:29:31,388] [pool-1-thread-2] Initializing /data/martin/Data1.cxd:
[testng] [2024-10-18 10:29:32,660] [pool-1-thread-7] Initializing /data/arvonn/Rat Fluor 2.cxd:
[testng] [2024-10-18 10:29:33,416] [pool-1-thread-12] Initializing /data/martin/XY-02.tif:
[testng] [2024-10-18 10:29:34,739] [pool-1-thread-8] Initializing /data/martin/XYT-01.tif:
[testng] [2024-10-18 10:29:35,868] [pool-1-thread-1] Initializing /data/hopi/#1YFP 0.96s gain5.tif:
[testng] [2024-10-18 10:29:37,131] [pool-1-thread-10] Initializing /data/martin/XY-ch-01.tif:
[testng] [2024-10-18 10:29:38,547] [pool-1-thread-9] Initializing /data/martin/HCI sample files/XYZT test.cxd:
[testng] [2024-10-18 10:29:39,100] [pool-1-thread-6] Initializing /data/cecilia/CoreScope/Test_50_100.cxd:
[testng] [2024-10-18 10:29:39,650] [pool-1-thread-3] Initializing /data/georg/GCamp3xtinCD4, GCamp3_99wmn_01_BT.cxd:
[testng] [2024-10-18 10:29:42,827] [pool-1-thread-5] Initializing /data/hopi/#2 2colors CFP0.36sgain1 YFP0.60sgain5.tif:
[testng] [2024-10-18 10:29:44,240] [pool-1-thread-2] Initializing /data/qa-11327/bone_tmp1981_00011.tif:
[testng] [2024-10-18 10:29:45,357] [pool-1-thread-4] Initializing /data/nico/b00/Image8.tif:
[testng] [2024-10-18 10:29:46,612] [pool-1-thread-11] Initializing /data/imagesc-90085/Data00042.cxd:
[testng] [2024-10-18 10:29:47,198] [pool-1-thread-7] Initializing /data/arvonn/3d Deconvolve Two Channel Sample.cxd:
[testng] [2024-10-18 10:29:49,052] [pool-1-thread-8] Initializing /data/arvonn/a rat 10x inverted qimaging 2 color 2000R-1.cxd:
[testng] [2024-10-18 10:29:49,959] [pool-1-thread-6] Initializing /data/ciprian/Pollen Band.cxd:
[testng] [2024-10-18 10:29:50,646] [pool-1-thread-9] 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: 4 minutes 22 seconds
Finished: SUCCESS