Started by upstream project "BIOFORMATS-test-repo" build number 212 originally caused by: Started by upstream project "Trigger" build number 238 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins6994404819084617406.sh + '[' cellsens = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_33721_merge_ci -v /uod/idr/repos/curated/cellsens:/data -v /uod/idr-scratch/merge-ci/curated/cellsens:/config snoopycrimecop/bioformats:merge_ci -Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR 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] 03:11:54,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:11:54,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:11:55,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:11:55,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:11:55,017 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:11:55,017 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:11:55,017 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:11:55,018 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:11:55,018 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@5c30a9b0 - End of configuration. [testng] 03:11:55,018 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@7a69b07 - Registering current configuration as safe fallback point [testng] 03:11:55,019 |-INFO in ch.qos.logback.classic.util.ContextInitializer@5e82df6a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 586 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-07 03:11:55,028] [main] java.version = 1.8.0_342 [testng] 03:11:55,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:11:55,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:11:55,090 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-07_03-11-55.log] [testng] 03:11:55,092 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-10-07 03:11:55,095] [main] testng.directory = /data [testng] [2024-10-07 03:11:55,096] [main] testng.configDirectory = /config [testng] [2024-10-07 03:11:55,116] [main] testng.multiplier = 1.0 [testng] [2024-10-07 03:11:55,116] [main] testng.in-memory = false [testng] [2024-10-07 03:11:55,117] [main] testng.allow-missing = false [testng] [2024-10-07 03:11:55,117] [main] user.language = fr [testng] [2024-10-07 03:11:55,117] [main] user.country = FR [testng] [2024-10-07 03:11:55,117] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-07 03:14:50,056] [main] ---------------------------------------- [testng] [2024-10-07 03:14:50,056] [main] Total files: 134 [testng] [2024-10-07 03:14:50,056] [main] Scan time: 174.939 s (1305 ms/file) [testng] [2024-10-07 03:14:50,056] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 72 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-07 03:15:22,068] [pool-1-thread-1] Initializing /data/samples/Fluorescence/Plant FL 100x 29 Z CI Decon2.vsi: [testng] 03:15:22,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:15:22,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:15:22,069 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-07_03-15-22.log] [testng] 03:15:22,070 |-INFO in ch.qos.logback.core.sift.SiftProcessor@114bbd1 - End of configuration. [testng] [2024-10-07 03:15:22,230] [pool-1-thread-12] Initializing /data/anda/Image_01_V76 K2 11_lung.thumbnail.jpg: [testng] 03:15:22,231 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:15:22,231 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:15:22,231 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-07_03-15-22.log] [testng] 03:15:22,232 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14c08ac3 - End of configuration. [testng] [2024-10-07 03:15:22,270] [pool-1-thread-11] Initializing /data/brian/SW10082402-02_21.vsi: [testng] 03:15:22,271 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:15:22,271 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:15:22,271 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-07_03-15-22.log] [testng] 03:15:22,272 |-INFO in ch.qos.logback.core.sift.SiftProcessor@598ecc79 - End of configuration. [testng] [2024-10-07 03:15:22,442] [pool-1-thread-10] Initializing /data/samples/Deconvolution/_chroma liver 40x 8 planes_/stack1/frame_t_0.ets: [testng] 03:15:22,442 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:15:22,442 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:15:22,443 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-07_03-15-22.log] [testng] 03:15:22,443 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35cd2ba7 - End of configuration. [testng] [2024-10-07 03:15:22,625] [pool-1-thread-9] Initializing /data/olivier/small-tiles/esgTS-+;Sox21a[6]-+_30D25_09.vsi: [testng] 03:15:22,625 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:15:22,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:15:22,626 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-07_03-15-22.log] [testng] 03:15:22,626 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5dd35354 - End of configuration. [testng] [2024-10-07 03:15:23,570] [pool-1-thread-8] Initializing /data/robert/Lung_Mite.vsi: [testng] 03:15:23,570 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:15:23,570 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:15:23,571 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-07_03-15-23.log] [testng] 03:15:23,571 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b1468d9 - End of configuration. [testng] [2024-10-07 03:15:23,927] [pool-1-thread-7] Initializing /data/qa-11039/Image_01.vsi: [testng] 03:15:23,927 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:15:23,927 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:15:23,928 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-07_03-15-23.log] [testng] 03:15:23,928 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c9aa0d9 - End of configuration. [testng] [2024-10-07 03:15:24,116] [pool-1-thread-6] Initializing /data/samples/Deconvolution/_islets_40X_2_/_islets_40X_2_/stack1/frame_t_0.ets: [testng] 03:15:24,117 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:15:24,117 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:15:24,118 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-07_03-15-24.log] [testng] 03:15:24,119 |-INFO in ch.qos.logback.core.sift.SiftProcessor@626cc06e - End of configuration. [testng] [2024-10-07 03:15:24,304] [pool-1-thread-5] Initializing /data/melissa/SW10082402-02_21 - cy2 - cy5 copy.vsi: [testng] 03:15:24,304 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:15:24,304 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:15:24,304 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-07_03-15-24.log] [testng] 03:15:24,305 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24f1923b - End of configuration. [testng] [2024-10-07 03:15:24,501] [pool-1-thread-4] Initializing /data/samples/Colocalisation/Daisy_Coloc.vsi: [testng] 03:15:24,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:15:24,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:15:24,502 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-07_03-15-24.log] [testng] 03:15:24,503 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58f8c44 - End of configuration. [testng] [2024-10-07 03:15:24,662] [pool-1-thread-3] Initializing /data/samples/Channels/svens cells - DIC.tif: [testng] 03:15:24,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:15:24,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:15:24,663 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-07_03-15-24.log] [testng] 03:15:24,663 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5bfe6898 - End of configuration. [testng] [2024-10-07 03:15:25,098] [pool-1-thread-2] Initializing /data/samples/Image SHOW/HER2_FISH Assay.tif: [testng] 03:15:25,098 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:15:25,098 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:15:25,098 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-07_03-15-25.log] [testng] 03:15:25,099 |-INFO in ch.qos.logback.core.sift.SiftProcessor@309b4437 - End of configuration. [testng] [2024-10-07 03:15:27,921] [pool-1-thread-12] Initializing /data/samples/Fluorescence Unmixing/HeLa_unmixed.tif: [testng] [2024-10-07 03:15:29,029] [pool-1-thread-8] Initializing /data/samples/Measurement & ROI/Oxyuranus_microlepidotus.tif: [testng] [2024-10-07 03:15:29,588] [pool-1-thread-4] Initializing /data/anthony/11R1398A1.vsi: [testng] [2024-10-07 03:15:30,004] [pool-1-thread-1] Initializing /data/qa-18870/Image_T30.vsi: [testng] [2024-10-07 03:15:30,380] [pool-1-thread-3] Initializing /data/david/Image_normal_skin with hair/Image_normal_skin with hair.vsi: [testng] [2024-10-07 03:15:30,687] [pool-1-thread-2] Initializing /data/olivier/14-09-2012/Image_07.vsi: [testng] [2024-10-07 03:15:31,061] [pool-1-thread-10] Initializing /data/samples/Deconvolution/Skin 2.tif: [testng] [2024-10-07 03:15:31,654] [pool-1-thread-6] Initializing /data/samples/Deconvolution/Silver birch raw.vsi: [testng] [2024-10-07 03:15:33,165] [pool-1-thread-8] Initializing /data/samples/Deconvolution/Gut section raw.vsi: [testng] [2024-10-07 03:15:33,470] [pool-1-thread-12] Initializing /data/anda/Image_01_V76 K2 11_lung.vsi: [testng] [2024-10-07 03:15:34,615] [pool-1-thread-6] Initializing /data/alex/pN1_new.vsi: [testng] [2024-10-07 03:15:35,233] [pool-1-thread-10] Initializing /data/brian/Image_28.vsi: [testng] [2024-10-07 03:15:37,094] [pool-1-thread-8] Initializing /data/samples/Process/HER2_FISH Assay.tif: [testng] [2024-10-07 03:15:43,316] [pool-1-thread-8] Initializing /data/samples/Shading Correction/Micrometer Background.tif: [testng] [2024-10-07 03:15:48,226] [pool-1-thread-8] Initializing /data/samples/Count & Measure/Cell Multichannel-z-stack corr..vsi: [testng] [2024-10-07 03:15:51,136] [pool-1-thread-8] Initializing /data/samples/Fluorescence/Dako_CISH.vsi: [testng] [2024-10-07 03:15:57,711] [pool-1-thread-8] Initializing /data/samples/Channels/svens cells - blue.tif: [testng] [2024-10-07 03:16:01,304] [pool-1-thread-8] Initializing /data/gh-3819/H30-18-endo-sost-40x.vsi: [testng] [2024-10-07 03:16:14,955] [pool-1-thread-6] Initializing /data/gh-3822/image.jp2: [testng] [2024-10-07 03:16:16,426] [pool-1-thread-8] Initializing /data/brian/BZ cfos1-2_05.vsi: [testng] [2024-10-07 03:16:16,942] [pool-1-thread-12] Initializing /data/samples/Measurement & ROI/Bandy Snake.tif: [testng] [2024-10-07 03:16:19,889] [pool-1-thread-12] Initializing /data/gh-3859/Image_Test2.vsi: [testng] [2024-10-07 03:16:23,453] [pool-1-thread-6] Initializing /data/olivier/Image_06.vsi: [testng] [2024-10-07 03:16:44,500] [pool-1-thread-8] Initializing /data/public/evident/Image_V4.1_FL_3D.vsi: [testng] [2024-10-07 03:16:46,809] [pool-1-thread-5] Initializing /data/public/evident/Image_V4.1_FL_2D.vsi: [testng] [2024-10-07 03:16:49,765] [pool-1-thread-11] Initializing /data/olivier/Stress47_02.vsi: [testng] [2024-10-07 03:16:52,446] [pool-1-thread-3] Initializing /data/qa-11394/f1 lateral 25hpf yen4 20X timelapse.vsi: [testng] [2024-10-07 03:16:55,238] [pool-1-thread-3] Initializing /data/johannes/PSF_green_1.vsi: [testng] [2024-10-07 03:16:57,714] [pool-1-thread-3] Initializing /data/samples/Image SHOW/Layer&Channels.tif: [testng] [2024-10-07 03:17:00,577] [pool-1-thread-3] Initializing /data/david/smithd_20111115_1.vsi: [testng] [2024-10-07 03:17:16,631] [pool-1-thread-6] Initializing /data/melissa/artificial-vsi/Image_V4.1_BF.vsi: [testng] [2024-10-07 03:17:50,467] [pool-1-thread-12] Initializing /data/olivier/7262 wt col.vsi: [testng] [2024-10-07 03:18:02,192] [pool-1-thread-11] Initializing /data/samples/Count & Measure/slide IHC.tif: [testng] [2024-10-07 03:18:05,484] [pool-1-thread-11] Initializing /data/samples/Measurement & ROI/Intensity t series.vsi: [testng] [2024-10-07 03:18:07,524] [pool-1-thread-11] Initializing /data/public/evident/Image_V4.1_BF.vsi: [testng] [2024-10-07 03:18:20,859] [pool-1-thread-10] Initializing /data/samples/Channels/svens cells - red.tif: [testng] [2024-10-07 03:18:23,843] [pool-1-thread-10] Initializing /data/melissa/SW10082402-02_21 - 1 - GOLD copy.vsi: [testng] [2024-10-07 03:18:58,037] [pool-1-thread-12] Initializing /data/qa-29751/VSI-import-example-file.vsi: [testng] [2024-10-07 03:19:00,088] [pool-1-thread-3] Initializing /data/samples/Measurement & ROI/Brown snake.tif: [testng] [2024-10-07 03:19:02,115] [pool-1-thread-3] Initializing /data/samples/Fluorescence Unmixing/HeLa_YFP_only.tif: [testng] [2024-10-07 03:19:04,371] [pool-1-thread-3] Initializing /data/michelle/FC(26)-19 Gadd45b 1hr_20121011_01.vsi: [testng] [2024-10-07 03:19:17,411] [pool-1-thread-8] Initializing /data/gh-3822/_image_/stack1/frame_t_0.ets: [testng] [2024-10-07 03:19:19,988] [pool-1-thread-2] Initializing /data/samples/Count & Measure/color squares.tif: [testng] [2024-10-07 03:19:21,816] [pool-1-thread-6] Initializing /data/samples/Process/Epithelial Cells3.tif: [testng] [2024-10-07 03:19:23,020] [pool-1-thread-10] Initializing /data/samples/Channels/Composite.vsi: [testng] [2024-10-07 03:19:23,471] [pool-1-thread-2] Initializing /data/samples/Fluorescence/drehung.avi: [testng] [2024-10-07 03:19:24,237] [pool-1-thread-6] Initializing /data/olivier/26-10-2014/Image_06.vsi: [testng] [2024-10-07 03:19:24,685] [pool-1-thread-2] Initializing /data/olivier/14-09-2012/Image_01.vsi: [testng] [2024-10-07 03:19:24,882] [pool-1-thread-10] Initializing /data/anda/Image_01_V76 K2 11_lung.overview.jpg: [testng] [2024-10-07 03:19:41,043] [pool-1-thread-10] Initializing /data/samples/Fluorescence Unmixing/HeLa_GFP_only.tif: [testng] [2024-10-07 03:19:42,095] [pool-1-thread-8] Initializing /data/olivier/26-10-2014/Image_27.vsi: [testng] [2024-10-07 03:19:43,108] [pool-1-thread-10] Initializing /data/alex/test.vsi: [testng] [2024-10-07 03:19:45,364] [pool-1-thread-10] Initializing /data/samples/Count & Measure/color dots.tif: [testng] [2024-10-07 03:19:47,738] [pool-1-thread-10] Initializing /data/samples/Count & Measure/Cell Multichannel-z-stack.vsi: [testng] [2024-10-07 03:19:48,461] [pool-1-thread-7] Initializing /data/samples/Shading Correction/Micrometer Original.tif: [testng] [2024-10-07 03:19:49,587] [pool-1-thread-10] Initializing /data/samples/Measurement & ROI/Snake.tif: [testng] [2024-10-07 03:19:50,712] [pool-1-thread-7] Initializing /data/samples/Fluorescence Unmixing/HeLa_original.tif: [testng] [2024-10-07 03:19:51,896] [pool-1-thread-10] Initializing /data/samples/Measurement & ROI/Cell Multichannel-M&R.tif: [testng] [2024-10-07 03:19:53,058] [pool-1-thread-7] Initializing /data/samples/Channels/svens cells - green.tif: [testng] [2024-10-07 03:19:54,264] [pool-1-thread-10] Initializing /data/olivier/26-10-2014/Image_27_2.vsi: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3816, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 14 minutes 22 seconds Finished: SUCCESS