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Started by upstream project "BIOFORMATS-test-repo" build number 273 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/jenkins12609733293354371486.sh + '[' simplepci = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_43021_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] 08:09:43,666 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 08:09:43,811 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 08:09:43,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 08:09:43,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 08:09:43,863 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 08:09:43,864 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 08:09:43,864 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 08:09:43,864 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 08:09:43,864 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1139b2f3 - End of configuration. [testng] 08:09:43,865 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@3f197a46 - Registering current configuration as safe fallback point [testng] 08:09:43,865 |-INFO in ch.qos.logback.classic.util.ContextInitializer@636be97c - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 596 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-29 08:09:43,876] [main] java.version = 1.8.0_342 [testng] 08:09:43,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 08:09:43,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:09:43,949 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-29_08-09-43.log] [testng] 08:09:43,951 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-29 08:09:43,978] [main] testng.directory = /data [testng] [2024-11-29 08:09:43,979] [main] testng.configDirectory = /config [testng] [2024-11-29 08:09:44,052] [main] testng.multiplier = 1.0 [testng] [2024-11-29 08:09:44,052] [main] testng.in-memory = false [testng] [2024-11-29 08:09:44,052] [main] testng.allow-missing = false [testng] [2024-11-29 08:09:44,052] [main] user.language = en [testng] [2024-11-29 08:09:44,052] [main] user.country = ${user.country} [testng] [2024-11-29 08:09:44,052] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-29 08:09:54,616] [main] ---------------------------------------- [testng] [2024-11-29 08:09:54,616] [main] Total files: 76 [testng] [2024-11-29 08:09:54,616] [main] Scan time: 10.564 s (139 ms/file) [testng] [2024-11-29 08:09:54,616] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 73 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-29 08:13:37,307] [pool-1-thread-1] Initializing /data/alessandro/Data1_1.cxd: [testng] 08:13:37,308 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 08:13:37,308 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:13:37,309 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-29_08-13-37.log] [testng] 08:13:37,309 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3cbe4df8 - End of configuration. [testng] [2024-11-29 08:13:38,764] [pool-1-thread-12] Initializing /data/jesper/1q35.cxd: [testng] 08:13:38,764 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 08:13:38,764 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:13:38,765 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-29_08-13-38.log] [testng] 08:13:38,765 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29fcacfb - End of configuration. [testng] [2024-11-29 08:13:39,972] [pool-1-thread-11] Initializing /data/martin/20090422bead20x_C2.ome.cxd: [testng] 08:13:39,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 08:13:39,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:13:39,973 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-29_08-13-39.log] [testng] 08:13:39,974 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fc5a249 - End of configuration. [testng] [2024-11-29 08:13:41,296] [pool-1-thread-10] Initializing /data/martin/XY-ch-02.tif: [testng] 08:13:41,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 08:13:41,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:13:41,297 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-29_08-13-41.log] [testng] 08:13:41,297 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ca14f18 - End of configuration. [testng] [2024-11-29 08:13:44,526] [pool-1-thread-9] Initializing /data/jcb/Test Run, 60 Sec PassesNEW.cxd: [testng] 08:13:44,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 08:13:44,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:13:44,527 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-29_08-13-44.log] [testng] 08:13:44,527 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1eed4bea - End of configuration. [testng] [2024-11-29 08:13:45,867] [pool-1-thread-8] Initializing /data/martin/20090422bead20x_C1.ome.cxd: [testng] 08:13:45,868 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 08:13:45,868 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:13:45,868 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-29_08-13-45.log] [testng] 08:13:45,869 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f6363c5 - End of configuration. [testng] [2024-11-29 08:13:47,059] [pool-1-thread-7] Initializing /data/martin/XY-03.tif: [testng] 08:13:47,059 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 08:13:47,059 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:13:47,060 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-29_08-13-47.log] [testng] 08:13:47,060 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f4cbd34 - End of configuration. [testng] [2024-11-29 08:13:50,073] [pool-1-thread-6] Initializing /data/martin/HCI sample files/XYT test 8x binning 286fps.cxd: [testng] 08:13:50,073 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 08:13:50,074 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:13:50,074 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-29_08-13-50.log] [testng] 08:13:50,075 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c30feb - End of configuration. [testng] [2024-11-29 08:13:51,636] [pool-1-thread-5] Initializing /data/martin/HCI sample files/test_2.tif: [testng] 08:13:51,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 08:13:51,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:13:51,637 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-29_08-13-51.log] [testng] 08:13:51,637 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6720c8fd - End of configuration. [testng] [2024-11-29 08:13:54,589] [pool-1-thread-4] Initializing /data/arvonn/gfpras_623.cxd: [testng] 08:13:54,589 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 08:13:54,589 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:13:54,590 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-29_08-13-54.log] [testng] 08:13:54,590 |-INFO in ch.qos.logback.core.sift.SiftProcessor@92b9339 - End of configuration. [testng] [2024-11-29 08:13:55,754] [pool-1-thread-3] Initializing /data/nico/b00/Image1.tif: [testng] 08:13:55,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 08:13:55,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:13:55,754 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-29_08-13-55.log] [testng] 08:13:55,755 |-INFO in ch.qos.logback.core.sift.SiftProcessor@bc91fe9 - End of configuration. [testng] [2024-11-29 08:13:58,745] [pool-1-thread-2] Initializing /data/cecilia/ts_05_13_10_5.cxd: [testng] 08:13:58,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 08:13:58,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:13:58,746 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-29_08-13-58.log] [testng] 08:13:58,746 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f8d2c84 - End of configuration. [testng] [2024-11-29 08:14:08,552] [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] [2024-11-29 08:14:11,293] [pool-1-thread-12] Initializing /data/nico/b00/Image7.tif: [testng] [2024-11-29 08:14:14,396] [pool-1-thread-4] Initializing /data/martin/XYT-01.cxd: [testng] [2024-11-29 08:14:15,602] [pool-1-thread-1] Initializing /data/arvonn/New Particles from Imants.cxd: [testng] [2024-11-29 08:14:16,877] [pool-1-thread-11] Initializing /data/martin/sample shift Mirella.cxd: [testng] [2024-11-29 08:14:18,055] [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] [2024-11-29 08:14:19,339] [pool-1-thread-9] Initializing /data/arvonn/good pollen 2z.cxd: [testng] [2024-11-29 08:14:20,522] [pool-1-thread-6] Initializing /data/hopi/3 channel/#7 image#1F1-34 10min per f 2f per s green.avi: [testng] [2024-11-29 08:14:22,609] [pool-1-thread-5] Initializing /data/martin/XY-01.tif: [testng] [2024-11-29 08:14:29,348] [pool-1-thread-6] Initializing /data/hopi/#1Hoechst 0.1s gain5.tif: [testng] [2024-11-29 08:14:32,711] [pool-1-thread-3] Initializing /data/nico/b00.cxd: [testng] [2024-11-29 08:14:35,169] [pool-1-thread-7] Initializing /data/nico/b00/Image4.tif: [testng] [2024-11-29 08:14:38,912] [pool-1-thread-10] Initializing /data/arvonn/gfpras2.avi: [testng] [2024-11-29 08:14:39,766] [pool-1-thread-4] Initializing /data/ciprian/Fura 2.cxd: [testng] [2024-11-29 08:14:41,410] [pool-1-thread-9] Initializing /data/gh-3625/no_timestamp_for_real.cxd: [testng] [2024-11-29 08:14:42,942] [pool-1-thread-11] Initializing /data/imagesc-72023/Data727.cxd: [testng] [2024-11-29 08:14:44,499] [pool-1-thread-1] Initializing /data/hopi/#2 phase.tif: [testng] [2024-11-29 08:14:47,716] [pool-1-thread-12] Initializing /data/cecilia/recheck_test2.cxd: [testng] [2024-11-29 08:14:49,552] [pool-1-thread-8] Initializing /data/nico/b00/Image2.tif: [testng] [2024-11-29 08:14:55,205] [pool-1-thread-10] Initializing /data/ciprian/Color Pollen.cxd: [testng] [2024-11-29 08:14:57,765] [pool-1-thread-3] Initializing /data/nico/b00/Image3.tif: [testng] [2024-11-29 08:15:03,618] [pool-1-thread-4] Initializing /data/imagesc-90085/VASA_PC2FISH1.cxd: [testng] [2024-11-29 08:15:06,215] [pool-1-thread-2] Initializing /data/hopi/#21 YFP filter.tif: [testng] [2024-11-29 08:15:12,386] [pool-1-thread-5] Initializing /data/qa-17305/image0_00021.tif: [testng] [2024-11-29 08:15:15,144] [pool-1-thread-11] Initializing /data/martin/HCI sample files/screenshot HCI.png: [testng] [2024-11-29 08:15:15,231] [pool-1-thread-6] Initializing /data/nico/b00/Image6.tif: [testng] [2024-11-29 08:15:18,372] [pool-1-thread-7] Initializing /data/ascb/030811RPE1.1x100DICData2nebd.cxd: [testng] [2024-11-29 08:15:21,060] [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] [2024-11-29 08:15:22,469] [pool-1-thread-12] Initializing /data/arvonn/fura.cxd: [testng] [2024-11-29 08:15:26,121] [pool-1-thread-11] Initializing /data/cecilia/CoreScope/Test_40_100.cxd: [testng] [2024-11-29 08:15:28,371] [pool-1-thread-10] Initializing /data/arvonn/shark.cxd: [testng] [2024-11-29 08:15:31,664] [pool-1-thread-8] Initializing /data/ciprian/Maggot color.tif: [testng] [2024-11-29 08:15:34,739] [pool-1-thread-1] Initializing /data/hopi/#21 two colors CFP(Red) YFP (green).tif: [testng] [2024-11-29 08:15:39,352] [pool-1-thread-4] Initializing /data/nico/b00/Image5.tif: [testng] [2024-11-29 08:15:42,450] [pool-1-thread-12] Initializing /data/arvonn/RG Z Beads.cxd: [testng] [2024-11-29 08:15:43,803] [pool-1-thread-3] Initializing /data/hopi/#21 CFP filter.tif: [testng] [2024-11-29 08:15:47,426] [pool-1-thread-9] Initializing /data/qa-11073/tinCD4 GCamp5 tdTomato DualView #1 488 only6.cxd: [testng] [2024-11-29 08:15:49,916] [pool-1-thread-11] Initializing /data/ben/Data1.cxd: [testng] [2024-11-29 08:15:51,495] [pool-1-thread-5] Initializing /data/hopi/3 channel/#7 image#1F1-34 10min per f 2f per s.avi: [testng] [2024-11-29 08:15:52,043] [pool-1-thread-6] Initializing /data/jcb/BEAF and SuHw 0.25M NaCl 5-11-12 #2.cxd: [testng] [2024-11-29 08:15:53,398] [pool-1-thread-2] Initializing /data/ciprian/fibroblast.tif: [testng] [2024-11-29 08:15:57,141] [pool-1-thread-7] Initializing /data/hopi/#21 phase.tif: [testng] [2024-11-29 08:16:03,459] [pool-1-thread-10] Initializing /data/arvonn/Point Spread Function 02um Bead TRITC.cxd: [testng] [2024-11-29 08:16:06,353] [pool-1-thread-12] Initializing /data/arvonn/gfpras2.cxd: [testng] [2024-11-29 08:16:07,969] [pool-1-thread-5] Initializing /data/martin/Data1.cxd: [testng] [2024-11-29 08:16:09,379] [pool-1-thread-11] Initializing /data/arvonn/Rat Fluor 2.cxd: [testng] [2024-11-29 08:16:11,092] [pool-1-thread-9] Initializing /data/martin/XY-02.tif: [testng] [2024-11-29 08:16:14,064] [pool-1-thread-8] Initializing /data/martin/XYT-01.tif: [testng] [2024-11-29 08:16:17,223] [pool-1-thread-1] Initializing /data/hopi/#1YFP 0.96s gain5.tif: [testng] [2024-11-29 08:16:20,193] [pool-1-thread-4] Initializing /data/martin/XY-ch-01.tif: [testng] [2024-11-29 08:16:23,336] [pool-1-thread-6] Initializing /data/cecilia/CoreScope/Test_50_100.cxd: [testng] [2024-11-29 08:16:24,088] [pool-1-thread-3] Initializing /data/martin/HCI sample files/XYZT test.cxd: [testng] [2024-11-29 08:16:27,975] [pool-1-thread-10] Initializing /data/georg/GCamp3xtinCD4, GCamp3_99wmn_01_BT.cxd: [testng] [2024-11-29 08:16:30,614] [pool-1-thread-12] Initializing /data/hopi/#2 2colors CFP0.36sgain1 YFP0.60sgain5.tif: [testng] [2024-11-29 08:16:33,686] [pool-1-thread-5] Initializing /data/qa-11327/bone_tmp1981_00011.tif: [testng] [2024-11-29 08:16:36,600] [pool-1-thread-2] Initializing /data/nico/b00/Image8.tif: [testng] [2024-11-29 08:16:39,780] [pool-1-thread-11] Initializing /data/arvonn/3d Deconvolve Two Channel Sample.cxd: [testng] [2024-11-29 08:16:41,233] [pool-1-thread-7] Initializing /data/imagesc-90085/Data00042.cxd: [testng] [2024-11-29 08:16:44,189] [pool-1-thread-8] Initializing /data/arvonn/a rat 10x inverted qimaging 2 color 2000R-1.cxd: [testng] [2024-11-29 08:16:46,761] [pool-1-thread-6] Initializing /data/ciprian/Pollen Band.cxd: [testng] [2024-11-29 08:16:48,533] [pool-1-thread-3] 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: 7 minutes 32 seconds Finished: SUCCESS