Started by upstream project "BIOFORMATS-test-repo" build number 190 originally caused by: Started by upstream project "Trigger" build number 212 originally caused by: Started by timer 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/jenkins16331906935720958606.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_30113_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] 02:37:13,329 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:37:13,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:37:13,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:37:13,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:37:13,444 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:37:13,445 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:37:13,445 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:37:13,446 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:37:13,446 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@5c30a9b0 - End of configuration. [testng] 02:37:13,447 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@7a69b07 - Registering current configuration as safe fallback point [testng] 02:37:13,448 |-INFO in ch.qos.logback.classic.util.ContextInitializer@5e82df6a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 455 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-16 02:37:13,467] [main] java.version = 1.8.0_342 [testng] 02:37:13,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:37:13,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:37:13,557 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-16_02-37-13.log] [testng] 02:37:13,560 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-09-16 02:37:13,564] [main] testng.directory = /data [testng] [2024-09-16 02:37:13,564] [main] testng.configDirectory = /config [testng] [2024-09-16 02:37:13,589] [main] testng.multiplier = 1.0 [testng] [2024-09-16 02:37:13,589] [main] testng.in-memory = false [testng] [2024-09-16 02:37:13,589] [main] testng.allow-missing = false [testng] [2024-09-16 02:37:13,590] [main] user.language = fr [testng] [2024-09-16 02:37:13,590] [main] user.country = FR [testng] [2024-09-16 02:37:13,590] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-09-16 02:40:02,442] [main] ---------------------------------------- [testng] [2024-09-16 02:40:02,442] [main] Total files: 134 [testng] [2024-09-16 02:40:02,442] [main] Scan time: 168.852 s (1260 ms/file) [testng] [2024-09-16 02:40:02,442] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 72 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-16 02:40:18,250] [pool-1-thread-1] Initializing /data/samples/Fluorescence/Plant FL 100x 29 Z CI Decon2.vsi: [testng] 02:40:18,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:40:18,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:18,252 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-16_02-40-18.log] [testng] 02:40:18,252 |-INFO in ch.qos.logback.core.sift.SiftProcessor@184b003a - End of configuration. [testng] [2024-09-16 02:40:18,312] [pool-1-thread-12] Initializing /data/anda/Image_01_V76 K2 11_lung.thumbnail.jpg: [testng] 02:40:18,313 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:40:18,313 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:18,313 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-16_02-40-18.log] [testng] 02:40:18,314 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72fd2c33 - End of configuration. [testng] [2024-09-16 02:40:18,326] [pool-1-thread-11] Initializing /data/brian/SW10082402-02_21.vsi: [testng] 02:40:18,326 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:40:18,326 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:18,327 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-16_02-40-18.log] [testng] 02:40:18,328 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d6b1cce - End of configuration. [testng] [2024-09-16 02:40:18,367] [pool-1-thread-10] Initializing /data/samples/Deconvolution/_chroma liver 40x 8 planes_/stack1/frame_t_0.ets: [testng] 02:40:18,367 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:40:18,367 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:18,368 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-16_02-40-18.log] [testng] 02:40:18,368 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3faa5875 - End of configuration. [testng] [2024-09-16 02:40:18,419] [pool-1-thread-9] Initializing /data/olivier/small-tiles/esgTS-+;Sox21a[6]-+_30D25_09.vsi: [testng] 02:40:18,420 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:40:18,420 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:18,420 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-16_02-40-18.log] [testng] 02:40:18,421 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ed6e66d - End of configuration. [testng] [2024-09-16 02:40:19,082] [pool-1-thread-8] Initializing /data/robert/Lung_Mite.vsi: [testng] 02:40:19,082 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:40:19,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:19,083 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-16_02-40-19.log] [testng] 02:40:19,083 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2124a725 - End of configuration. [testng] [2024-09-16 02:40:19,308] [pool-1-thread-7] Initializing /data/qa-11039/Image_01.vsi: [testng] 02:40:19,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:40:19,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:19,309 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-16_02-40-19.log] [testng] 02:40:19,310 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b052704 - End of configuration. [testng] [2024-09-16 02:40:19,385] [pool-1-thread-6] Initializing /data/samples/Deconvolution/_islets_40X_2_/_islets_40X_2_/stack1/frame_t_0.ets: [testng] 02:40:19,385 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:40:19,385 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:19,386 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-16_02-40-19.log] [testng] 02:40:19,386 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59ebc553 - End of configuration. [testng] [2024-09-16 02:40:19,447] [pool-1-thread-5] Initializing /data/melissa/SW10082402-02_21 - cy2 - cy5 copy.vsi: [testng] 02:40:19,448 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:40:19,448 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:19,448 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-16_02-40-19.log] [testng] 02:40:19,449 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34a955bd - End of configuration. [testng] [2024-09-16 02:40:19,498] [pool-1-thread-4] Initializing /data/samples/Colocalisation/Daisy_Coloc.vsi: [testng] 02:40:19,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:40:19,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:19,499 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-16_02-40-19.log] [testng] 02:40:19,499 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a748a7a - End of configuration. [testng] [2024-09-16 02:40:19,536] [pool-1-thread-3] Initializing /data/samples/Channels/svens cells - DIC.tif: [testng] 02:40:19,536 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:40:19,536 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:19,537 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-16_02-40-19.log] [testng] 02:40:19,537 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4423cfd8 - End of configuration. [testng] [2024-09-16 02:40:19,635] [pool-1-thread-2] Initializing /data/samples/Image SHOW/HER2_FISH Assay.tif: [testng] 02:40:19,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:40:19,635 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:19,636 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-16_02-40-19.log] [testng] 02:40:19,636 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a9cd1c2 - End of configuration. [testng] [2024-09-16 02:40:21,179] [pool-1-thread-12] Initializing /data/samples/Fluorescence Unmixing/HeLa_unmixed.tif: [testng] [2024-09-16 02:40:21,739] [pool-1-thread-4] Initializing /data/samples/Measurement & ROI/Oxyuranus_microlepidotus.tif: [testng] [2024-09-16 02:40:21,791] [pool-1-thread-1] Initializing /data/anthony/11R1398A1.vsi: [testng] [2024-09-16 02:40:21,913] [pool-1-thread-8] Initializing /data/qa-18870/Image_T30.vsi: [testng] [2024-09-16 02:40:22,275] [pool-1-thread-3] Initializing /data/david/Image_normal_skin with hair/Image_normal_skin with hair.vsi: [testng] [2024-09-16 02:40:22,324] [pool-1-thread-2] Initializing /data/samples/Deconvolution/Silver birch raw.vsi: [testng] [2024-09-16 02:40:22,352] [pool-1-thread-6] Initializing /data/samples/Deconvolution/Skin 2.tif: [testng] [2024-09-16 02:40:22,461] [pool-1-thread-10] Initializing /data/olivier/14-09-2012/Image_07.vsi: [testng] [2024-09-16 02:40:23,013] [pool-1-thread-12] Initializing /data/samples/Deconvolution/Gut section raw.vsi: [testng] [2024-09-16 02:40:23,151] [pool-1-thread-4] Initializing /data/anda/Image_01_V76 K2 11_lung.vsi: [testng] [2024-09-16 02:40:23,355] [pool-1-thread-2] Initializing /data/alex/pN1_new.vsi: [testng] [2024-09-16 02:40:23,407] [pool-1-thread-6] Initializing /data/brian/Image_28.vsi: [testng] [2024-09-16 02:40:24,767] [pool-1-thread-12] Initializing /data/samples/Process/HER2_FISH Assay.tif: [testng] [2024-09-16 02:40:26,672] [pool-1-thread-12] Initializing /data/samples/Shading Correction/Micrometer Background.tif: [testng] [2024-09-16 02:40:28,155] [pool-1-thread-12] Initializing /data/samples/Count & Measure/Cell Multichannel-z-stack corr..vsi: [testng] [2024-09-16 02:40:29,507] [pool-1-thread-12] Initializing /data/samples/Fluorescence/Dako_CISH.vsi: [testng] [2024-09-16 02:40:34,777] [pool-1-thread-4] Initializing /data/samples/Channels/svens cells - blue.tif: [testng] [2024-09-16 02:40:35,897] [pool-1-thread-12] Initializing /data/gh-3819/H30-18-endo-sost-40x.vsi: [testng] [2024-09-16 02:40:36,312] [pool-1-thread-4] Initializing /data/gh-3822/image.jp2: [testng] [2024-09-16 02:40:43,499] [pool-1-thread-4] Initializing /data/brian/BZ cfos1-2_05.vsi: [testng] [2024-09-16 02:40:44,450] [pool-1-thread-2] Initializing /data/samples/Measurement & ROI/Bandy Snake.tif: [testng] [2024-09-16 02:40:45,374] [pool-1-thread-12] Initializing /data/gh-3859/Image_Test2.vsi: [testng] [2024-09-16 02:40:45,916] [pool-1-thread-2] Initializing /data/olivier/Image_06.vsi: [testng] [2024-09-16 02:40:54,432] [pool-1-thread-4] Initializing /data/public/evident/Image_V4.1_FL_3D.vsi: [testng] [2024-09-16 02:41:13,384] [pool-1-thread-3] Initializing /data/public/evident/Image_V4.1_FL_2D.vsi: [testng] [2024-09-16 02:41:27,473] [pool-1-thread-5] Initializing /data/olivier/Stress47_02.vsi: [testng] [2024-09-16 02:41:31,053] [pool-1-thread-11] Initializing /data/qa-11394/f1 lateral 25hpf yen4 20X timelapse.vsi: [testng] [2024-09-16 02:41:32,527] [pool-1-thread-11] Initializing /data/johannes/PSF_green_1.vsi: [testng] [2024-09-16 02:41:33,749] [pool-1-thread-2] Initializing /data/samples/Image SHOW/Layer&Channels.tif: [testng] [2024-09-16 02:41:33,922] [pool-1-thread-11] Initializing /data/david/smithd_20111115_1.vsi: [testng] [2024-09-16 02:41:36,136] [pool-1-thread-2] Initializing /data/melissa/artificial-vsi/Image_V4.1_BF.vsi: [testng] [2024-09-16 02:42:04,677] [pool-1-thread-12] Initializing /data/olivier/7262 wt col.vsi: [testng] [2024-09-16 02:42:27,146] [pool-1-thread-5] Initializing /data/samples/Count & Measure/slide IHC.tif: [testng] [2024-09-16 02:42:28,725] [pool-1-thread-5] Initializing /data/samples/Measurement & ROI/Intensity t series.vsi: [testng] [2024-09-16 02:42:30,125] [pool-1-thread-5] Initializing /data/public/evident/Image_V4.1_BF.vsi: [testng] [2024-09-16 02:42:48,168] [pool-1-thread-6] Initializing /data/samples/Channels/svens cells - red.tif: [testng] [2024-09-16 02:42:49,437] [pool-1-thread-6] Initializing /data/melissa/SW10082402-02_21 - 1 - GOLD copy.vsi: [testng] [2024-09-16 02:43:14,026] [pool-1-thread-11] Initializing /data/qa-29751/VSI-import-example-file.vsi: [testng] [2024-09-16 02:43:20,535] [pool-1-thread-4] Initializing /data/samples/Measurement & ROI/Brown snake.tif: [testng] [2024-09-16 02:43:21,609] [pool-1-thread-4] Initializing /data/samples/Fluorescence Unmixing/HeLa_YFP_only.tif: [testng] [2024-09-16 02:43:22,449] [pool-1-thread-4] Initializing /data/michelle/FC(26)-19 Gadd45b 1hr_20121011_01.vsi: [testng] [2024-09-16 02:43:24,450] [pool-1-thread-12] Initializing /data/gh-3822/_image_/stack1/frame_t_0.ets: [testng] [2024-09-16 02:43:40,464] [pool-1-thread-2] Initializing /data/samples/Count & Measure/color squares.tif: [testng] [2024-09-16 02:43:42,261] [pool-1-thread-2] Initializing /data/samples/Process/Epithelial Cells3.tif: [testng] [2024-09-16 02:43:43,182] [pool-1-thread-12] Initializing /data/samples/Channels/Composite.vsi: [testng] [2024-09-16 02:43:43,402] [pool-1-thread-2] Initializing /data/samples/Fluorescence/drehung.avi: [testng] [2024-09-16 02:43:44,341] [pool-1-thread-2] Initializing /data/olivier/26-10-2014/Image_06.vsi: [testng] [2024-09-16 02:43:44,558] [pool-1-thread-12] Initializing /data/olivier/14-09-2012/Image_01.vsi: [testng] [2024-09-16 02:43:47,909] [pool-1-thread-6] Initializing /data/anda/Image_01_V76 K2 11_lung.overview.jpg: [testng] [2024-09-16 02:44:04,534] [pool-1-thread-1] Initializing /data/samples/Fluorescence Unmixing/HeLa_GFP_only.tif: [testng] [2024-09-16 02:44:05,168] [pool-1-thread-1] Initializing /data/olivier/26-10-2014/Image_27.vsi: [testng] [2024-09-16 02:44:06,697] [pool-1-thread-6] Initializing /data/alex/test.vsi: [testng] [2024-09-16 02:44:07,972] [pool-1-thread-6] Initializing /data/samples/Count & Measure/color dots.tif: [testng] [2024-09-16 02:44:09,316] [pool-1-thread-6] Initializing /data/samples/Count & Measure/Cell Multichannel-z-stack.vsi: [testng] [2024-09-16 02:44:10,642] [pool-1-thread-6] Initializing /data/samples/Shading Correction/Micrometer Original.tif: [testng] [2024-09-16 02:44:12,105] [pool-1-thread-6] Initializing /data/samples/Measurement & ROI/Snake.tif: [testng] [2024-09-16 02:44:13,036] [pool-1-thread-6] Initializing /data/samples/Fluorescence Unmixing/HeLa_original.tif: [testng] [2024-09-16 02:44:14,319] [pool-1-thread-6] Initializing /data/samples/Measurement & ROI/Cell Multichannel-M&R.tif: [testng] [2024-09-16 02:44:15,696] [pool-1-thread-6] Initializing /data/samples/Channels/svens cells - green.tif: [testng] [2024-09-16 02:44:16,889] [pool-1-thread-6] 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: 11 minutes 28 seconds Finished: SUCCESS