Started by upstream project "BIOFORMATS-test-repo" build number 18 originally caused by: Started by upstream project "Trigger" build number 21 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/jenkins8140861585884748061.sh + '[' cellsens = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_2225_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] 02:18:28,451 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:18:28,477 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:18:28,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:18:28,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:18:28,504 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:18:28,504 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:18:28,504 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:18:28,505 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:18:28,505 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@5e600dd5 - End of configuration. [testng] 02:18:28,505 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@a38c7fe - Registering current configuration as safe fallback point [testng] 02:18:28,505 |-INFO in ch.qos.logback.classic.util.ContextInitializer@6fdbe764 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 374 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-31 02:18:28,515] [main] java.version = 17.0.2 [testng] 02:18:28,518 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:18:28,518 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:28,558 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-31_02-18-28.log] [testng] 02:18:28,559 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-03-31 02:18:28,562] [main] testng.directory = /data [testng] [2024-03-31 02:18:28,562] [main] testng.configDirectory = /config [testng] [2024-03-31 02:18:28,589] [main] testng.multiplier = 1.0 [testng] [2024-03-31 02:18:28,590] [main] testng.in-memory = false [testng] [2024-03-31 02:18:28,591] [main] testng.allow-missing = false [testng] [2024-03-31 02:18:28,591] [main] user.language = en [testng] [2024-03-31 02:18:28,591] [main] user.country = ${user.country} [testng] [2024-03-31 02:18:28,591] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-31 02:20:42,071] [main] ---------------------------------------- [testng] [2024-03-31 02:20:42,071] [main] Total files: 134 [testng] [2024-03-31 02:20:42,071] [main] Scan time: 133.48 s (996 ms/file) [testng] [2024-03-31 02:20:42,071] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 72 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-31 02:20:58,438] [pool-1-thread-1] Initializing /data/melissa/artificial-vsi/Image_V4.1_BF.vsi: [testng] 02:20:58,439 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:20:58,439 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:58,440 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-31_02-20-58.log] [testng] 02:20:58,440 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6aba0af3 - End of configuration. [testng] [2024-03-31 02:20:58,516] [pool-1-thread-12] Initializing /data/samples/Count & Measure/Cell Multichannel-z-stack corr..vsi: [testng] 02:20:58,517 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:20:58,517 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:58,517 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-31_02-20-58.log] [testng] 02:20:58,518 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32cc429d - End of configuration. [testng] [2024-03-31 02:20:58,661] [pool-1-thread-11] Initializing /data/olivier/26-10-2014/Image_06.vsi: [testng] 02:20:58,661 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:20:58,661 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:58,662 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-31_02-20-58.log] [testng] 02:20:58,663 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1044fb86 - End of configuration. [testng] [2024-03-31 02:20:58,740] [pool-1-thread-10] Initializing /data/samples/Measurement & ROI/Bandy Snake.tif: [testng] 02:20:58,740 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:20:58,740 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:58,741 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-31_02-20-58.log] [testng] 02:20:58,742 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26424174 - End of configuration. [testng] [2024-03-31 02:20:58,846] [pool-1-thread-9] Initializing /data/brian/BZ cfos1-2_05.vsi: [testng] 02:20:58,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:20:58,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:58,848 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-31_02-20-58.log] [testng] 02:20:58,848 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12f1944e - End of configuration. [testng] [2024-03-31 02:20:58,905] [pool-1-thread-8] Initializing /data/samples/Measurement & ROI/Intensity t series.vsi: [testng] 02:20:58,906 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:20:58,906 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:58,906 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-31_02-20-58.log] [testng] 02:20:58,907 |-INFO in ch.qos.logback.core.sift.SiftProcessor@384e365a - End of configuration. [testng] [2024-03-31 02:20:58,949] [pool-1-thread-7] Initializing /data/qa-18870/Image_T30.vsi: [testng] 02:20:58,950 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:20:58,950 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:58,951 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-31_02-20-58.log] [testng] 02:20:58,951 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ed86ded - End of configuration. [testng] [2024-03-31 02:20:59,025] [pool-1-thread-6] Initializing /data/gh-3822/_image_/stack1/frame_t_0.ets: [testng] 02:20:59,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:20:59,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:59,026 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-31_02-20-59.log] [testng] 02:20:59,027 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42f4caeb - End of configuration. [testng] [2024-03-31 02:20:59,080] [pool-1-thread-5] Initializing /data/melissa/SW10082402-02_21 - cy2 - cy5 copy.vsi: [testng] 02:20:59,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:20:59,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:59,081 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-31_02-20-59.log] [testng] 02:20:59,082 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b357b08 - End of configuration. [testng] [2024-03-31 02:20:59,121] [pool-1-thread-4] Initializing /data/samples/Measurement & ROI/Brown snake.tif: [testng] 02:20:59,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:20:59,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:59,122 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-31_02-20-59.log] [testng] 02:20:59,123 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4800223e - End of configuration. [testng] [2024-03-31 02:20:59,216] [pool-1-thread-3] Initializing /data/alex/pN1_new.vsi: [testng] 02:20:59,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:20:59,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:59,217 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-31_02-20-59.log] [testng] 02:20:59,218 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54c1f843 - End of configuration. [testng] [2024-03-31 02:20:59,256] [pool-1-thread-2] Initializing /data/public/evident/Image_V4.1_FL_2D.vsi: [testng] 02:20:59,256 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:20:59,256 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:59,257 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-31_02-20-59.log] [testng] 02:20:59,257 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63b33184 - End of configuration. [testng] [2024-03-31 02:21:02,192] [pool-1-thread-4] Initializing /data/samples/Shading Correction/Micrometer Original.tif: [testng] [2024-03-31 02:21:02,302] [pool-1-thread-8] Initializing /data/melissa/SW10082402-02_21 - 1 - GOLD copy.vsi: [testng] [2024-03-31 02:21:02,336] [pool-1-thread-10] Initializing /data/samples/Deconvolution/Gut section raw.vsi: [testng] [2024-03-31 02:21:02,372] [pool-1-thread-12] Initializing /data/qa-11394/f1 lateral 25hpf yen4 20X timelapse.vsi: [testng] [2024-03-31 02:21:04,155] [pool-1-thread-4] Initializing /data/samples/Process/Epithelial Cells3.tif: [testng] [2024-03-31 02:21:04,259] [pool-1-thread-10] Initializing /data/samples/Colocalisation/Daisy_Coloc.vsi: [testng] [2024-03-31 02:21:04,552] [pool-1-thread-12] Initializing /data/samples/Measurement & ROI/Oxyuranus_microlepidotus.tif: [testng] [2024-03-31 02:21:05,087] [pool-1-thread-4] Initializing /data/qa-11039/Image_01.vsi: [testng] [2024-03-31 02:21:05,248] [pool-1-thread-10] Initializing /data/anda/Image_01_V76 K2 11_lung.thumbnail.jpg: [testng] [2024-03-31 02:21:05,481] [pool-1-thread-10] Initializing /data/samples/Channels/svens cells - green.tif: [testng] [2024-03-31 02:21:05,520] [pool-1-thread-12] Initializing /data/samples/Deconvolution/_islets_40X_2_/_islets_40X_2_/stack1/frame_t_0.ets: [testng] [2024-03-31 02:21:06,543] [pool-1-thread-10] Initializing /data/olivier/14-09-2012/Image_07.vsi: [testng] [2024-03-31 02:21:07,042] [pool-1-thread-12] Initializing /data/samples/Channels/svens cells - DIC.tif: [testng] [2024-03-31 02:21:07,977] [pool-1-thread-12] Initializing /data/samples/Channels/svens cells - red.tif: [testng] [2024-03-31 02:21:09,120] [pool-1-thread-12] Initializing /data/samples/Count & Measure/color squares.tif: [testng] [2024-03-31 02:21:10,504] [pool-1-thread-12] Initializing /data/public/evident/Image_V4.1_BF.vsi: [testng] [2024-03-31 02:21:17,723] [pool-1-thread-3] Initializing /data/samples/Count & Measure/color dots.tif: [testng] [2024-03-31 02:21:19,028] [pool-1-thread-3] Initializing /data/samples/Image SHOW/HER2_FISH Assay.tif: [testng] [2024-03-31 02:21:19,374] [pool-1-thread-6] Initializing /data/samples/Deconvolution/_chroma liver 40x 8 planes_/stack1/frame_t_0.ets: [testng] [2024-03-31 02:21:20,780] [pool-1-thread-3] Initializing /data/olivier/26-10-2014/Image_27.vsi: [testng] [2024-03-31 02:21:21,531] [pool-1-thread-6] Initializing /data/samples/Fluorescence Unmixing/HeLa_GFP_only.tif: [testng] [2024-03-31 02:21:22,026] [pool-1-thread-6] Initializing /data/olivier/Image_06.vsi: [testng] [2024-03-31 02:21:27,127] [pool-1-thread-9] Initializing /data/gh-3859/Image_Test2.vsi: [testng] [2024-03-31 02:21:49,752] [pool-1-thread-8] Initializing /data/olivier/Stress47_02.vsi: [testng] [2024-03-31 02:22:02,139] [pool-1-thread-5] Initializing /data/samples/Fluorescence Unmixing/HeLa_YFP_only.tif: [testng] [2024-03-31 02:22:02,659] [pool-1-thread-5] Initializing /data/samples/Measurement & ROI/Snake.tif: [testng] [2024-03-31 02:22:03,422] [pool-1-thread-5] Initializing /data/samples/Deconvolution/Skin 2.tif: [testng] [2024-03-31 02:22:04,119] [pool-1-thread-5] Initializing /data/samples/Fluorescence/drehung.avi: [testng] [2024-03-31 02:22:04,711] [pool-1-thread-5] Initializing /data/brian/Image_28.vsi: [testng] [2024-03-31 02:22:05,356] [pool-1-thread-6] Initializing /data/david/smithd_20111115_1.vsi: [testng] [2024-03-31 02:22:36,858] [pool-1-thread-11] Initializing /data/samples/Deconvolution/Silver birch raw.vsi: [testng] [2024-03-31 02:22:37,523] [pool-1-thread-11] Initializing /data/anda/Image_01_V76 K2 11_lung.vsi: [testng] [2024-03-31 02:22:42,655] [pool-1-thread-8] Initializing /data/samples/Count & Measure/Cell Multichannel-z-stack.vsi: [testng] [2024-03-31 02:22:43,959] [pool-1-thread-8] Initializing /data/samples/Fluorescence/Plant FL 100x 29 Z CI Decon2.vsi: [testng] [2024-03-31 02:22:44,986] [pool-1-thread-8] Initializing /data/anthony/11R1398A1.vsi: [testng] [2024-03-31 02:22:55,673] [pool-1-thread-3] Initializing /data/gh-3822/image.jp2: [testng] [2024-03-31 02:22:57,202] [pool-1-thread-9] Initializing /data/michelle/FC(26)-19 Gadd45b 1hr_20121011_01.vsi: [testng] [2024-03-31 02:23:00,942] [pool-1-thread-3] Initializing /data/robert/Lung_Mite.vsi: [testng] [2024-03-31 02:23:02,490] [pool-1-thread-3] Initializing /data/olivier/7262 wt col.vsi: [testng] [2024-03-31 02:23:06,628] [pool-1-thread-11] Initializing /data/public/evident/Image_V4.1_FL_3D.vsi: [testng] [2024-03-31 02:23:14,779] [pool-1-thread-12] Initializing /data/samples/Count & Measure/slide IHC.tif: [testng] [2024-03-31 02:23:16,040] [pool-1-thread-12] Initializing /data/samples/Fluorescence Unmixing/HeLa_original.tif: [testng] [2024-03-31 02:23:17,114] [pool-1-thread-12] Initializing /data/brian/SW10082402-02_21.vsi: [testng] [2024-03-31 02:23:20,897] [pool-1-thread-1] Initializing /data/johannes/PSF_green_1.vsi: [testng] [2024-03-31 02:23:22,075] [pool-1-thread-1] Initializing /data/samples/Process/HER2_FISH Assay.tif: [testng] [2024-03-31 02:23:23,298] [pool-1-thread-1] Initializing /data/olivier/14-09-2012/Image_01.vsi: [testng] [2024-03-31 02:23:36,377] [pool-1-thread-6] Initializing /data/samples/Channels/svens cells - blue.tif: [testng] [2024-03-31 02:23:37,188] [pool-1-thread-6] Initializing /data/alex/test.vsi: [testng] [2024-03-31 02:23:38,335] [pool-1-thread-6] Initializing /data/qa-29751/VSI-import-example-file.vsi: [testng] [2024-03-31 02:24:13,559] [pool-1-thread-3] Initializing /data/samples/Fluorescence Unmixing/HeLa_unmixed.tif: [testng] [2024-03-31 02:24:15,392] [pool-1-thread-3] Initializing /data/david/Image_normal_skin with hair/Image_normal_skin with hair.vsi: [testng] [2024-03-31 02:24:25,926] [pool-1-thread-12] Initializing /data/olivier/small-tiles/esgTS-+;Sox21a[6]-+_30D25_09.vsi: [testng] [2024-03-31 02:24:30,234] [pool-1-thread-5] Initializing /data/anda/Image_01_V76 K2 11_lung.overview.jpg: [testng] [2024-03-31 02:24:48,373] [pool-1-thread-10] Initializing /data/gh-3819/H30-18-endo-sost-40x.vsi: [testng] [2024-03-31 02:24:59,257] [pool-1-thread-5] Initializing /data/samples/Fluorescence/Dako_CISH.vsi: [testng] [2024-03-31 02:25:05,267] [pool-1-thread-10] Initializing /data/samples/Channels/Composite.vsi: [testng] [2024-03-31 02:25:06,111] [pool-1-thread-5] Initializing /data/samples/Image SHOW/Layer&Channels.tif: [testng] [2024-03-31 02:25:07,584] [pool-1-thread-10] Initializing /data/samples/Shading Correction/Micrometer Background.tif: [testng] [2024-03-31 02:25:08,770] [pool-1-thread-10] Initializing /data/samples/Measurement & ROI/Cell Multichannel-M&R.tif: [testng] [2024-03-31 02:25:09,308] [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: 16 minutes 31 seconds Finished: SUCCESS