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Started by upstream project "BIOFORMATS-test-repo" build number 110 originally caused by: Started by upstream project "Trigger" build number 123 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/jenkins8443838400269239229.sh + '[' cellsens = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_17150_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 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 [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] 1 warning test-automated: [testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 02:11:04,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:11:04,421 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:11:04,444 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:11:04,444 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:11:04,450 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:11:04,450 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:11:04,450 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:11:04,451 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:11:04,451 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@5e600dd5 - End of configuration. [testng] 02:11:04,458 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@a38c7fe - Registering current configuration as safe fallback point [testng] 02:11:04,458 |-INFO in ch.qos.logback.classic.util.ContextInitializer@6fdbe764 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 419 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-03 02:11:04,468] [main] java.version = 17.0.2 [testng] 02:11:04,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:11:04,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:04,512 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-03_02-11-04.log] [testng] 02:11:04,513 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-07-03 02:11:04,515] [main] testng.directory = /data [testng] [2024-07-03 02:11:04,515] [main] testng.configDirectory = /config [testng] [2024-07-03 02:11:04,571] [main] testng.multiplier = 1.0 [testng] [2024-07-03 02:11:04,571] [main] testng.in-memory = false [testng] [2024-07-03 02:11:04,572] [main] testng.allow-missing = false [testng] [2024-07-03 02:11:04,572] [main] user.language = en [testng] [2024-07-03 02:11:04,572] [main] user.country = ${user.country} [testng] [2024-07-03 02:11:04,572] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-03 02:13:07,969] [main] ---------------------------------------- [testng] [2024-07-03 02:13:07,969] [main] Total files: 134 [testng] [2024-07-03 02:13:07,969] [main] Scan time: 123.397 s (920 ms/file) [testng] [2024-07-03 02:13:07,969] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 72 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-03 02:13:21,102] [pool-1-thread-1] Initializing /data/melissa/artificial-vsi/Image_V4.1_BF.vsi: [testng] 02:13:21,103 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:13:21,103 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:21,104 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-03_02-13-21.log] [testng] 02:13:21,105 |-INFO in ch.qos.logback.core.sift.SiftProcessor@108dad3b - End of configuration. [testng] [2024-07-03 02:13:21,160] [pool-1-thread-12] Initializing /data/samples/Count & Measure/Cell Multichannel-z-stack corr..vsi: [testng] 02:13:21,160 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:13:21,160 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:21,161 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-03_02-13-21.log] [testng] 02:13:21,162 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6143e3c1 - End of configuration. [testng] [2024-07-03 02:13:21,242] [pool-1-thread-11] Initializing /data/olivier/26-10-2014/Image_06.vsi: [testng] 02:13:21,242 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:13:21,242 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:21,243 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-03_02-13-21.log] [testng] 02:13:21,244 |-INFO in ch.qos.logback.core.sift.SiftProcessor@486445c4 - End of configuration. [testng] [2024-07-03 02:13:21,295] [pool-1-thread-10] Initializing /data/samples/Measurement & ROI/Bandy Snake.tif: [testng] 02:13:21,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:13:21,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:21,296 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-03_02-13-21.log] [testng] 02:13:21,297 |-INFO in ch.qos.logback.core.sift.SiftProcessor@384e365a - End of configuration. [testng] [2024-07-03 02:13:21,358] [pool-1-thread-9] Initializing /data/brian/BZ cfos1-2_05.vsi: [testng] 02:13:21,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:13:21,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:21,360 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-03_02-13-21.log] [testng] 02:13:21,360 |-INFO in ch.qos.logback.core.sift.SiftProcessor@640417 - End of configuration. [testng] [2024-07-03 02:13:21,398] [pool-1-thread-8] Initializing /data/samples/Measurement & ROI/Intensity t series.vsi: [testng] 02:13:21,398 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:13:21,398 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:21,399 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-03_02-13-21.log] [testng] 02:13:21,400 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50eab307 - End of configuration. [testng] [2024-07-03 02:13:21,448] [pool-1-thread-7] Initializing /data/qa-18870/Image_T30.vsi: [testng] 02:13:21,448 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:13:21,448 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:21,449 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-03_02-13-21.log] [testng] 02:13:21,449 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68380114 - End of configuration. [testng] [2024-07-03 02:13:21,498] [pool-1-thread-6] Initializing /data/gh-3822/_image_/stack1/frame_t_0.ets: [testng] 02:13:21,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:13:21,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:21,499 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-03_02-13-21.log] [testng] 02:13:21,499 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39d874cf - End of configuration. [testng] [2024-07-03 02:13:21,523] [pool-1-thread-5] Initializing /data/melissa/SW10082402-02_21 - cy2 - cy5 copy.vsi: [testng] 02:13:21,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:13:21,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:21,525 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-03_02-13-21.log] [testng] 02:13:21,525 |-INFO in ch.qos.logback.core.sift.SiftProcessor@214d6121 - End of configuration. [testng] [2024-07-03 02:13:21,563] [pool-1-thread-4] Initializing /data/samples/Measurement & ROI/Brown snake.tif: [testng] 02:13:21,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:13:21,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:21,565 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-03_02-13-21.log] [testng] 02:13:21,565 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f20e4ab - End of configuration. [testng] [2024-07-03 02:13:21,630] [pool-1-thread-3] Initializing /data/alex/pN1_new.vsi: [testng] 02:13:21,630 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:13:21,630 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:21,631 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-03_02-13-21.log] [testng] 02:13:21,632 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4adebc7 - End of configuration. [testng] [2024-07-03 02:13:21,687] [pool-1-thread-2] Initializing /data/public/evident/Image_V4.1_FL_2D.vsi: [testng] 02:13:21,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:13:21,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:21,688 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-03_02-13-21.log] [testng] 02:13:21,688 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7de36794 - End of configuration. [testng] [2024-07-03 02:13:25,081] [pool-1-thread-4] Initializing /data/samples/Shading Correction/Micrometer Original.tif: [testng] [2024-07-03 02:13:25,136] [pool-1-thread-8] Initializing /data/melissa/SW10082402-02_21 - 1 - GOLD copy.vsi: [testng] [2024-07-03 02:13:25,163] [pool-1-thread-10] Initializing /data/samples/Deconvolution/Gut section raw.vsi: [testng] [2024-07-03 02:13:25,192] [pool-1-thread-12] Initializing /data/qa-11394/f1 lateral 25hpf yen4 20X timelapse.vsi: [testng] [2024-07-03 02:13:26,375] [pool-1-thread-4] Initializing /data/samples/Process/Epithelial Cells3.tif: [testng] [2024-07-03 02:13:26,643] [pool-1-thread-10] Initializing /data/samples/Colocalisation/Daisy_Coloc.vsi: [testng] [2024-07-03 02:13:27,139] [pool-1-thread-12] Initializing /data/samples/Measurement & ROI/Oxyuranus_microlepidotus.tif: [testng] [2024-07-03 02:13:27,298] [pool-1-thread-4] Initializing /data/qa-11039/Image_01.vsi: [testng] [2024-07-03 02:13:27,600] [pool-1-thread-10] Initializing /data/anda/Image_01_V76 K2 11_lung.thumbnail.jpg: [testng] [2024-07-03 02:13:27,892] [pool-1-thread-10] Initializing /data/samples/Channels/svens cells - green.tif: [testng] [2024-07-03 02:13:27,950] [pool-1-thread-12] Initializing /data/samples/Deconvolution/_islets_40X_2_/_islets_40X_2_/stack1/frame_t_0.ets: [testng] [2024-07-03 02:13:28,880] [pool-1-thread-10] Initializing /data/olivier/14-09-2012/Image_07.vsi: [testng] [2024-07-03 02:13:29,449] [pool-1-thread-12] Initializing /data/samples/Channels/svens cells - DIC.tif: [testng] [2024-07-03 02:13:30,331] [pool-1-thread-12] Initializing /data/samples/Channels/svens cells - red.tif: [testng] [2024-07-03 02:13:31,324] [pool-1-thread-12] Initializing /data/samples/Count & Measure/color squares.tif: [testng] [2024-07-03 02:13:32,601] [pool-1-thread-12] Initializing /data/public/evident/Image_V4.1_BF.vsi: [testng] [2024-07-03 02:13:41,449] [pool-1-thread-3] Initializing /data/samples/Count & Measure/color dots.tif: [testng] [2024-07-03 02:13:42,135] [pool-1-thread-6] Initializing /data/samples/Image SHOW/HER2_FISH Assay.tif: [testng] [2024-07-03 02:13:42,867] [pool-1-thread-3] Initializing /data/samples/Deconvolution/_chroma liver 40x 8 planes_/stack1/frame_t_0.ets: [testng] [2024-07-03 02:13:43,478] [pool-1-thread-6] Initializing /data/olivier/26-10-2014/Image_27.vsi: [testng] [2024-07-03 02:13:44,863] [pool-1-thread-3] Initializing /data/samples/Fluorescence Unmixing/HeLa_GFP_only.tif: [testng] [2024-07-03 02:13:45,321] [pool-1-thread-3] Initializing /data/olivier/Image_06.vsi: [testng] [2024-07-03 02:13:51,393] [pool-1-thread-9] Initializing /data/gh-3859/Image_Test2.vsi: [testng] [2024-07-03 02:14:13,167] [pool-1-thread-8] Initializing /data/olivier/Stress47_02.vsi: [testng] [2024-07-03 02:14:21,760] [pool-1-thread-5] Initializing /data/samples/Fluorescence Unmixing/HeLa_YFP_only.tif: [testng] [2024-07-03 02:14:22,260] [pool-1-thread-5] Initializing /data/samples/Measurement & ROI/Snake.tif: [testng] [2024-07-03 02:14:23,033] [pool-1-thread-5] Initializing /data/samples/Deconvolution/Skin 2.tif: [testng] [2024-07-03 02:14:23,611] [pool-1-thread-5] Initializing /data/samples/Fluorescence/drehung.avi: [testng] [2024-07-03 02:14:24,121] [pool-1-thread-5] Initializing /data/brian/Image_28.vsi: [testng] [2024-07-03 02:14:25,144] [pool-1-thread-3] Initializing /data/david/smithd_20111115_1.vsi: [testng] [2024-07-03 02:14:42,727] [pool-1-thread-11] Initializing /data/samples/Deconvolution/Silver birch raw.vsi: [testng] [2024-07-03 02:14:43,353] [pool-1-thread-11] Initializing /data/anda/Image_01_V76 K2 11_lung.vsi: [testng] [2024-07-03 02:14:50,488] [pool-1-thread-11] Initializing /data/samples/Count & Measure/Cell Multichannel-z-stack.vsi: [testng] [2024-07-03 02:14:51,438] [pool-1-thread-11] Initializing /data/samples/Fluorescence/Plant FL 100x 29 Z CI Decon2.vsi: [testng] [2024-07-03 02:14:52,339] [pool-1-thread-11] Initializing /data/anthony/11R1398A1.vsi: [testng] [2024-07-03 02:14:56,045] [pool-1-thread-8] Initializing /data/gh-3822/image.jp2: [testng] [2024-07-03 02:15:01,183] [pool-1-thread-8] Initializing /data/michelle/FC(26)-19 Gadd45b 1hr_20121011_01.vsi: [testng] [2024-07-03 02:15:04,297] [pool-1-thread-6] Initializing /data/robert/Lung_Mite.vsi: [testng] [2024-07-03 02:15:05,829] [pool-1-thread-6] Initializing /data/olivier/7262 wt col.vsi: [testng] [2024-07-03 02:15:08,897] [pool-1-thread-9] Initializing /data/public/evident/Image_V4.1_FL_3D.vsi: [testng] [2024-07-03 02:15:17,664] [pool-1-thread-12] Initializing /data/samples/Count & Measure/slide IHC.tif: [testng] [2024-07-03 02:15:18,148] [pool-1-thread-1] Initializing /data/samples/Fluorescence Unmixing/HeLa_original.tif: [testng] [2024-07-03 02:15:18,884] [pool-1-thread-12] Initializing /data/brian/SW10082402-02_21.vsi: [testng] [2024-07-03 02:15:19,054] [pool-1-thread-1] Initializing /data/johannes/PSF_green_1.vsi: [testng] [2024-07-03 02:15:20,022] [pool-1-thread-1] Initializing /data/samples/Process/HER2_FISH Assay.tif: [testng] [2024-07-03 02:15:21,435] [pool-1-thread-1] Initializing /data/olivier/14-09-2012/Image_01.vsi: [testng] [2024-07-03 02:15:54,380] [pool-1-thread-3] Initializing /data/samples/Channels/svens cells - blue.tif: [testng] [2024-07-03 02:15:55,256] [pool-1-thread-3] Initializing /data/alex/test.vsi: [testng] [2024-07-03 02:15:56,634] [pool-1-thread-3] Initializing /data/qa-29751/VSI-import-example-file.vsi: [testng] [2024-07-03 02:16:20,412] [pool-1-thread-12] Initializing /data/samples/Fluorescence Unmixing/HeLa_unmixed.tif: [testng] [2024-07-03 02:16:21,216] [pool-1-thread-12] Initializing /data/david/Image_normal_skin with hair/Image_normal_skin with hair.vsi: [testng] [2024-07-03 02:16:21,419] [pool-1-thread-6] Initializing /data/olivier/small-tiles/esgTS-+;Sox21a[6]-+_30D25_09.vsi: [testng] [2024-07-03 02:16:22,103] [pool-1-thread-5] Initializing /data/anda/Image_01_V76 K2 11_lung.overview.jpg: [testng] [2024-07-03 02:16:36,144] [pool-1-thread-5] Initializing /data/gh-3819/H30-18-endo-sost-40x.vsi: [testng] [2024-07-03 02:16:44,246] [pool-1-thread-5] Initializing /data/samples/Fluorescence/Dako_CISH.vsi: [testng] [2024-07-03 02:16:49,455] [pool-1-thread-5] Initializing /data/samples/Channels/Composite.vsi: [testng] [2024-07-03 02:16:50,335] [pool-1-thread-5] Initializing /data/samples/Image SHOW/Layer&Channels.tif: [testng] [2024-07-03 02:16:51,406] [pool-1-thread-5] Initializing /data/samples/Shading Correction/Micrometer Background.tif: [testng] [2024-07-03 02:16:52,065] [pool-1-thread-5] Initializing /data/samples/Measurement & ROI/Cell Multichannel-M&R.tif: [testng] [2024-07-03 02:16:52,976] [pool-1-thread-5] 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: 13 minutes 51 seconds Finished: SUCCESS