![[Jenkins]](/jenkins/static/d0200910/images/svgs/logo.svg){kind=logo}
Started by upstream project "BIOFORMATS-test-repo" build number 62 originally caused by: Started by upstream project "Trigger" build number 69 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins16715933189661654231.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_9278_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] 02:22:08,982 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:22:09,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:22:09,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:22:09,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:22:09,070 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:22:09,070 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:22:09,070 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:22:09,070 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:22:09,070 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@5c30a9b0 - End of configuration. [testng] 02:22:09,071 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@7a69b07 - Registering current configuration as safe fallback point [testng] 02:22:09,071 |-INFO in ch.qos.logback.classic.util.ContextInitializer@5e82df6a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 400 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-13 02:22:09,081] [main] java.version = 1.8.0_342 [testng] 02:22:09,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:22:09,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:22:09,130 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-13_02-22-09.log] [testng] 02:22:09,132 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-05-13 02:22:09,134] [main] testng.directory = /data [testng] [2024-05-13 02:22:09,134] [main] testng.configDirectory = /config [testng] [2024-05-13 02:22:09,170] [main] testng.multiplier = 1.0 [testng] [2024-05-13 02:22:09,170] [main] testng.in-memory = false [testng] [2024-05-13 02:22:09,170] [main] testng.allow-missing = false [testng] [2024-05-13 02:22:09,170] [main] user.language = fr [testng] [2024-05-13 02:22:09,170] [main] user.country = FR [testng] [2024-05-13 02:22:09,170] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-05-13 02:24:38,482] [main] ---------------------------------------- [testng] [2024-05-13 02:24:38,483] [main] Total files: 134 [testng] [2024-05-13 02:24:38,483] [main] Scan time: 149.312 s (1114 ms/file) [testng] [2024-05-13 02:24:38,483] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 72 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-13 02:24:52,867] [pool-1-thread-1] Initializing /data/samples/Measurement & ROI/Brown snake.tif: [testng] 02:24:52,867 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:24:52,867 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:24:52,869 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-13_02-24-52.log] [testng] 02:24:52,869 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39398d67 - End of configuration. [testng] [2024-05-13 02:24:52,924] [pool-1-thread-12] Initializing /data/melissa/SW10082402-02_21 - cy2 - cy5 copy.vsi: [testng] 02:24:52,925 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:24:52,925 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:24:52,927 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-13_02-24-52.log] [testng] 02:24:52,928 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73e1918e - End of configuration. [testng] [2024-05-13 02:24:52,966] [pool-1-thread-11] Initializing /data/samples/Image SHOW/HER2_FISH Assay.tif: [testng] 02:24:52,967 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:24:52,967 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:24:52,968 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-13_02-24-52.log] [testng] 02:24:52,968 |-INFO in ch.qos.logback.core.sift.SiftProcessor@702f6152 - End of configuration. [testng] [2024-05-13 02:24:53,109] [pool-1-thread-10] Initializing /data/samples/Channels/Composite.vsi: [testng] 02:24:53,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:24:53,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:24:53,111 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-13_02-24-53.log] [testng] 02:24:53,111 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2020bb4f - End of configuration. [testng] [2024-05-13 02:24:53,151] [pool-1-thread-9] Initializing /data/brian/SW10082402-02_21.vsi: [testng] 02:24:53,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:24:53,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:24:53,151 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-13_02-24-53.log] [testng] 02:24:53,152 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a871f4e - End of configuration. [testng] [2024-05-13 02:24:53,210] [pool-1-thread-8] Initializing /data/samples/Count & Measure/color dots.tif: [testng] 02:24:53,210 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:24:53,211 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:24:53,211 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-13_02-24-53.log] [testng] 02:24:53,211 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a437853 - End of configuration. [testng] [2024-05-13 02:24:53,262] [pool-1-thread-7] Initializing /data/samples/Channels/svens cells - red.tif: [testng] 02:24:53,262 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:24:53,262 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:24:53,262 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-13_02-24-53.log] [testng] 02:24:53,263 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b2acafd - End of configuration. [testng] [2024-05-13 02:24:53,310] [pool-1-thread-6] Initializing /data/samples/Image SHOW/Layer&Channels.tif: [testng] 02:24:53,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:24:53,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:24:53,311 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-13_02-24-53.log] [testng] 02:24:53,312 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2cfa63c6 - End of configuration. [testng] [2024-05-13 02:24:53,384] [pool-1-thread-5] Initializing /data/olivier/Image_06.vsi: [testng] 02:24:53,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:24:53,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:24:53,385 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-13_02-24-53.log] [testng] 02:24:53,385 |-INFO in ch.qos.logback.core.sift.SiftProcessor@366f8c14 - End of configuration. [testng] [2024-05-13 02:24:53,412] [pool-1-thread-4] Initializing /data/samples/Deconvolution/_chroma liver 40x 8 planes_/stack1/frame_t_0.ets: [testng] 02:24:53,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:24:53,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:24:53,412 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-13_02-24-53.log] [testng] 02:24:53,413 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36f61657 - End of configuration. [testng] [2024-05-13 02:24:53,433] [pool-1-thread-3] Initializing /data/samples/Count & Measure/slide IHC.tif: [testng] 02:24:53,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:24:53,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:24:53,434 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-13_02-24-53.log] [testng] 02:24:53,435 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58096bcf - End of configuration. [testng] [2024-05-13 02:24:53,480] [pool-1-thread-2] Initializing /data/samples/Process/HER2_FISH Assay.tif: [testng] 02:24:53,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:24:53,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:24:53,481 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-13_02-24-53.log] [testng] 02:24:53,481 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2995353b - End of configuration. [testng] [2024-05-13 02:24:56,464] [pool-1-thread-3] Initializing /data/gh-3822/_image_/stack1/frame_t_0.ets: [testng] [2024-05-13 02:24:56,483] [pool-1-thread-10] Initializing /data/samples/Fluorescence Unmixing/HeLa_YFP_only.tif: [testng] [2024-05-13 02:24:56,529] [pool-1-thread-1] Initializing /data/samples/Fluorescence Unmixing/HeLa_original.tif: [testng] [2024-05-13 02:24:56,617] [pool-1-thread-8] Initializing /data/samples/Fluorescence Unmixing/HeLa_unmixed.tif: [testng] [2024-05-13 02:24:56,697] [pool-1-thread-2] Initializing /data/public/evident/Image_V4.1_FL_2D.vsi: [testng] [2024-05-13 02:24:56,734] [pool-1-thread-6] Initializing /data/melissa/artificial-vsi/Image_V4.1_BF.vsi: [testng] [2024-05-13 02:24:56,776] [pool-1-thread-7] Initializing /data/samples/Count & Measure/Cell Multichannel-z-stack corr..vsi: [testng] [2024-05-13 02:24:56,896] [pool-1-thread-4] Initializing /data/gh-3859/Image_Test2.vsi: [testng] [2024-05-13 02:24:56,948] [pool-1-thread-11] Initializing /data/samples/Process/Epithelial Cells3.tif: [testng] [2024-05-13 02:24:58,073] [pool-1-thread-11] Initializing /data/alex/test.vsi: [testng] [2024-05-13 02:24:58,098] [pool-1-thread-10] Initializing /data/gh-3822/image.jp2: [testng] [2024-05-13 02:24:58,286] [pool-1-thread-8] Initializing /data/david/Image_normal_skin with hair/Image_normal_skin with hair.vsi: [testng] [2024-05-13 02:24:58,480] [pool-1-thread-1] Initializing /data/melissa/SW10082402-02_21 - 1 - GOLD copy.vsi: [testng] [2024-05-13 02:24:58,549] [pool-1-thread-7] Initializing /data/samples/Deconvolution/_islets_40X_2_/_islets_40X_2_/stack1/frame_t_0.ets: [testng] [2024-05-13 02:24:59,696] [pool-1-thread-11] Initializing /data/samples/Measurement & ROI/Bandy Snake.tif: [testng] [2024-05-13 02:25:00,201] [pool-1-thread-7] Initializing /data/samples/Deconvolution/Gut section raw.vsi: [testng] [2024-05-13 02:25:01,214] [pool-1-thread-11] Initializing /data/olivier/14-09-2012/Image_01.vsi: [testng] [2024-05-13 02:25:01,634] [pool-1-thread-7] Initializing /data/olivier/26-10-2014/Image_06.vsi: [testng] [2024-05-13 02:25:05,457] [pool-1-thread-10] Initializing /data/johannes/PSF_green_1.vsi: [testng] [2024-05-13 02:25:06,804] [pool-1-thread-10] Initializing /data/samples/Shading Correction/Micrometer Original.tif: [testng] [2024-05-13 02:25:07,590] [pool-1-thread-10] Initializing /data/anda/Image_01_V76 K2 11_lung.overview.jpg: [testng] [2024-05-13 02:25:19,794] [pool-1-thread-3] Initializing /data/olivier/26-10-2014/Image_27.vsi: [testng] [2024-05-13 02:25:27,012] [pool-1-thread-10] Initializing /data/anda/Image_01_V76 K2 11_lung.thumbnail.jpg: [testng] [2024-05-13 02:25:27,197] [pool-1-thread-10] Initializing /data/qa-29751/VSI-import-example-file.vsi: [testng] [2024-05-13 02:25:44,712] [pool-1-thread-5] Initializing /data/samples/Channels/svens cells - green.tif: [testng] [2024-05-13 02:25:45,652] [pool-1-thread-5] Initializing /data/samples/Channels/svens cells - blue.tif: [testng] [2024-05-13 02:25:46,650] [pool-1-thread-5] Initializing /data/robert/Lung_Mite.vsi: [testng] [2024-05-13 02:25:48,508] [pool-1-thread-5] Initializing /data/samples/Colocalisation/Daisy_Coloc.vsi: [testng] [2024-05-13 02:25:49,335] [pool-1-thread-5] Initializing /data/olivier/26-10-2014/Image_27_2.vsi: [testng] [2024-05-13 02:25:55,675] [pool-1-thread-1] Initializing /data/samples/Shading Correction/Micrometer Background.tif: [testng] [2024-05-13 02:25:56,691] [pool-1-thread-1] Initializing /data/michelle/FC(26)-19 Gadd45b 1hr_20121011_01.vsi: [testng] [2024-05-13 02:26:02,225] [pool-1-thread-8] Initializing /data/brian/BZ cfos1-2_05.vsi: [testng] [2024-05-13 02:26:04,542] [pool-1-thread-12] Initializing /data/olivier/Stress47_02.vsi: [testng] [2024-05-13 02:26:09,159] [pool-1-thread-9] Initializing /data/qa-18870/Image_T30.vsi: [testng] [2024-05-13 02:26:27,671] [pool-1-thread-4] Initializing /data/samples/Fluorescence Unmixing/HeLa_GFP_only.tif: [testng] [2024-05-13 02:26:27,834] [pool-1-thread-8] Initializing /data/samples/Channels/svens cells - DIC.tif: [testng] [2024-05-13 02:26:28,189] [pool-1-thread-4] Initializing /data/samples/Deconvolution/Skin 2.tif: [testng] [2024-05-13 02:26:28,714] [pool-1-thread-8] Initializing /data/olivier/7262 wt col.vsi: [testng] [2024-05-13 02:26:28,878] [pool-1-thread-4] Initializing /data/samples/Count & Measure/Cell Multichannel-z-stack.vsi: [testng] [2024-05-13 02:26:30,747] [pool-1-thread-4] Initializing /data/samples/Measurement & ROI/Oxyuranus_microlepidotus.tif: [testng] [2024-05-13 02:26:32,195] [pool-1-thread-4] Initializing /data/olivier/small-tiles/esgTS-+;Sox21a[6]-+_30D25_09.vsi: [testng] [2024-05-13 02:26:52,078] [pool-1-thread-7] Initializing /data/olivier/14-09-2012/Image_07.vsi: [testng] [2024-05-13 02:27:06,860] [pool-1-thread-6] Initializing /data/samples/Fluorescence/drehung.avi: [testng] [2024-05-13 02:27:07,497] [pool-1-thread-6] Initializing /data/samples/Count & Measure/color squares.tif: [testng] [2024-05-13 02:27:08,006] [pool-1-thread-3] Initializing /data/samples/Measurement & ROI/Cell Multichannel-M&R.tif: [testng] [2024-05-13 02:27:08,907] [pool-1-thread-6] Initializing /data/public/evident/Image_V4.1_FL_3D.vsi: [testng] [2024-05-13 02:27:09,412] [pool-1-thread-3] Initializing /data/brian/Image_28.vsi: [testng] [2024-05-13 02:27:10,245] [pool-1-thread-12] Initializing /data/public/evident/Image_V4.1_BF.vsi: [testng] [2024-05-13 02:27:17,725] [pool-1-thread-8] Initializing /data/gh-3819/H30-18-endo-sost-40x.vsi: [testng] [2024-05-13 02:27:26,970] [pool-1-thread-8] Initializing /data/alex/pN1_new.vsi: [testng] [2024-05-13 02:27:29,863] [pool-1-thread-5] Initializing /data/anthony/11R1398A1.vsi: [testng] [2024-05-13 02:27:40,854] [pool-1-thread-8] Initializing /data/anda/Image_01_V76 K2 11_lung.vsi: [testng] [2024-05-13 02:27:41,456] [pool-1-thread-8] Initializing /data/samples/Measurement & ROI/Intensity t series.vsi: [testng] [2024-05-13 02:27:42,441] [pool-1-thread-8] Initializing /data/qa-11039/Image_01.vsi: [testng] [2024-05-13 02:27:53,429] [pool-1-thread-10] Initializing /data/david/smithd_20111115_1.vsi: [testng] [2024-05-13 02:27:57,141] [pool-1-thread-11] Initializing /data/samples/Fluorescence/Plant FL 100x 29 Z CI Decon2.vsi: [testng] [2024-05-13 02:27:58,050] [pool-1-thread-11] Initializing /data/samples/Fluorescence/Dako_CISH.vsi: [testng] [2024-05-13 02:28:06,236] [pool-1-thread-11] Initializing /data/samples/Measurement & ROI/Snake.tif: [testng] [2024-05-13 02:28:07,624] [pool-1-thread-11] Initializing /data/samples/Deconvolution/Silver birch raw.vsi: [testng] [2024-05-13 02:28:09,042] [pool-1-thread-11] Initializing /data/qa-11394/f1 lateral 25hpf yen4 20X timelapse.vsi: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3816, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 13 minutes 32 seconds Finished: SUCCESS