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Started by upstream project "BIOFORMATS-test-repo" build number 54 originally caused by: Started by upstream project "Trigger" build number 61 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins5904480544270910496.sh + '[' cellsens = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_7966_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] 02:19:26,096 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:19:26,155 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:19:26,177 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:19:26,177 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:19:26,182 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:19:26,182 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:19:26,182 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:19:26,183 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:19:26,183 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@5e600dd5 - End of configuration. [testng] 02:19:26,184 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@a38c7fe - Registering current configuration as safe fallback point [testng] 02:19:26,184 |-INFO in ch.qos.logback.classic.util.ContextInitializer@6fdbe764 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 452 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-05 02:19:26,193] [main] java.version = 17.0.2 [testng] 02:19:26,196 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:19:26,196 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:19:26,505 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-05_02-19-26.log] [testng] 02:19:26,506 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-05-05 02:19:26,508] [main] testng.directory = /data [testng] [2024-05-05 02:19:26,509] [main] testng.configDirectory = /config [testng] [2024-05-05 02:19:26,537] [main] testng.multiplier = 1.0 [testng] [2024-05-05 02:19:26,538] [main] testng.in-memory = false [testng] [2024-05-05 02:19:26,538] [main] testng.allow-missing = false [testng] [2024-05-05 02:19:26,538] [main] user.language = en [testng] [2024-05-05 02:19:26,538] [main] user.country = ${user.country} [testng] [2024-05-05 02:19:26,538] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-05-05 02:21:23,635] [main] ---------------------------------------- [testng] [2024-05-05 02:21:23,635] [main] Total files: 134 [testng] [2024-05-05 02:21:23,635] [main] Scan time: 117.097 s (873 ms/file) [testng] [2024-05-05 02:21:23,635] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 72 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-05 02:21:38,911] [pool-1-thread-1] Initializing /data/gh-3822/_image_/stack1/frame_t_0.ets: [testng] 02:21:38,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:21:38,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:21:38,912 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-05_02-21-38.log] [testng] 02:21:38,913 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5519b9e6 - End of configuration. [testng] [2024-05-05 02:21:38,958] [pool-1-thread-12] Initializing /data/samples/Measurement & ROI/Intensity t series.vsi: [testng] 02:21:38,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:21:38,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:21:38,959 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-05_02-21-38.log] [testng] 02:21:38,960 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14060539 - End of configuration. [testng] [2024-05-05 02:21:38,985] [pool-1-thread-11] Initializing /data/samples/Channels/Composite.vsi: [testng] 02:21:38,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:21:38,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:21:38,986 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-05_02-21-38.log] [testng] 02:21:38,986 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a7f7f68 - End of configuration. [testng] [2024-05-05 02:21:39,020] [pool-1-thread-10] Initializing /data/melissa/SW10082402-02_21 - 1 - GOLD copy.vsi: [testng] 02:21:39,020 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:21:39,020 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:21:39,021 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-05_02-21-39.log] [testng] 02:21:39,021 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34a53221 - End of configuration. [testng] [2024-05-05 02:21:39,054] [pool-1-thread-9] Initializing /data/samples/Fluorescence Unmixing/HeLa_GFP_only.tif: [testng] 02:21:39,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:21:39,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:21:39,055 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-05_02-21-39.log] [testng] 02:21:39,055 |-INFO in ch.qos.logback.core.sift.SiftProcessor@640417 - End of configuration. [testng] [2024-05-05 02:21:39,118] [pool-1-thread-8] Initializing /data/alex/pN1_new.vsi: [testng] 02:21:39,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:21:39,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:21:39,119 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-05_02-21-39.log] [testng] 02:21:39,119 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43e24e86 - End of configuration. [testng] [2024-05-05 02:21:39,156] [pool-1-thread-7] Initializing /data/samples/Fluorescence Unmixing/HeLa_unmixed.tif: [testng] 02:21:39,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:21:39,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:21:39,157 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-05_02-21-39.log] [testng] 02:21:39,158 |-INFO in ch.qos.logback.core.sift.SiftProcessor@605226a0 - End of configuration. [testng] [2024-05-05 02:21:39,293] [pool-1-thread-6] Initializing /data/olivier/small-tiles/esgTS-+;Sox21a[6]-+_30D25_09.vsi: [testng] 02:21:39,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:21:39,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:21:39,294 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-05_02-21-39.log] [testng] 02:21:39,295 |-INFO in ch.qos.logback.core.sift.SiftProcessor@430ab9ae - End of configuration. [testng] [2024-05-05 02:21:39,939] [pool-1-thread-5] Initializing /data/brian/BZ cfos1-2_05.vsi: [testng] 02:21:39,939 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:21:39,939 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:21:39,940 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-05_02-21-39.log] [testng] 02:21:39,940 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53cab0b2 - End of configuration. [testng] [2024-05-05 02:21:39,957] [pool-1-thread-4] Initializing /data/gh-3819/H30-18-endo-sost-40x.vsi: [testng] 02:21:39,957 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:21:39,957 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:21:39,958 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-05_02-21-39.log] [testng] 02:21:39,958 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ca5ae24 - End of configuration. [testng] [2024-05-05 02:21:39,973] [pool-1-thread-3] Initializing /data/samples/Fluorescence Unmixing/HeLa_YFP_only.tif: [testng] 02:21:39,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:21:39,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:21:39,974 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-05_02-21-39.log] [testng] 02:21:39,974 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48c409b - End of configuration. [testng] [2024-05-05 02:21:40,017] [pool-1-thread-2] Initializing /data/olivier/26-10-2014/Image_27_2.vsi: [testng] 02:21:40,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:21:40,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:21:40,018 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-05_02-21-40.log] [testng] 02:21:40,019 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c994552 - End of configuration. [testng] [2024-05-05 02:21:42,331] [pool-1-thread-3] Initializing /data/samples/Measurement & ROI/Snake.tif: [testng] [2024-05-05 02:21:42,400] [pool-1-thread-9] Initializing /data/samples/Measurement & ROI/Bandy Snake.tif: [testng] [2024-05-05 02:21:42,471] [pool-1-thread-7] Initializing /data/david/smithd_20111115_1.vsi: [testng] [2024-05-05 02:21:42,553] [pool-1-thread-11] Initializing /data/samples/Colocalisation/Daisy_Coloc.vsi: [testng] [2024-05-05 02:21:42,579] [pool-1-thread-12] Initializing /data/olivier/Stress47_02.vsi: [testng] [2024-05-05 02:21:43,488] [pool-1-thread-3] Initializing /data/robert/Lung_Mite.vsi: [testng] [2024-05-05 02:21:43,643] [pool-1-thread-11] Initializing /data/samples/Image SHOW/HER2_FISH Assay.tif: [testng] [2024-05-05 02:21:43,827] [pool-1-thread-9] Initializing /data/olivier/Image_06.vsi: [testng] [2024-05-05 02:21:45,028] [pool-1-thread-3] Initializing /data/qa-18870/Image_T30.vsi: [testng] [2024-05-05 02:21:45,059] [pool-1-thread-11] Initializing /data/samples/Count & Measure/color squares.tif: [testng] [2024-05-05 02:21:46,255] [pool-1-thread-11] Initializing /data/samples/Process/Epithelial Cells3.tif: [testng] [2024-05-05 02:21:46,959] [pool-1-thread-11] Initializing /data/johannes/PSF_green_1.vsi: [testng] [2024-05-05 02:21:48,024] [pool-1-thread-11] Initializing /data/qa-11039/Image_01.vsi: [testng] [2024-05-05 02:21:51,029] [pool-1-thread-4] Initializing /data/qa-29751/VSI-import-example-file.vsi: [testng] [2024-05-05 02:21:54,974] [pool-1-thread-8] Initializing /data/samples/Channels/svens cells - green.tif: [testng] [2024-05-05 02:21:55,805] [pool-1-thread-8] Initializing /data/samples/Measurement & ROI/Oxyuranus_microlepidotus.tif: [testng] [2024-05-05 02:21:56,568] [pool-1-thread-8] Initializing /data/olivier/26-10-2014/Image_27.vsi: [testng] [2024-05-05 02:21:58,145] [pool-1-thread-1] Initializing /data/samples/Channels/svens cells - blue.tif: [testng] [2024-05-05 02:21:59,129] [pool-1-thread-1] Initializing /data/samples/Fluorescence/Plant FL 100x 29 Z CI Decon2.vsi: [testng] [2024-05-05 02:22:00,062] [pool-1-thread-1] Initializing /data/samples/Count & Measure/color dots.tif: [testng] [2024-05-05 02:22:01,263] [pool-1-thread-1] Initializing /data/melissa/SW10082402-02_21 - cy2 - cy5 copy.vsi: [testng] [2024-05-05 02:22:05,226] [pool-1-thread-5] Initializing /data/samples/Deconvolution/Skin 2.tif: [testng] [2024-05-05 02:22:05,948] [pool-1-thread-5] Initializing /data/olivier/14-09-2012/Image_01.vsi: [testng] [2024-05-05 02:22:25,309] [pool-1-thread-9] Initializing /data/brian/SW10082402-02_21.vsi: [testng] [2024-05-05 02:22:30,774] [pool-1-thread-12] Initializing /data/olivier/14-09-2012/Image_07.vsi: [testng] [2024-05-05 02:22:33,827] [pool-1-thread-10] Initializing /data/samples/Deconvolution/_chroma liver 40x 8 planes_/stack1/frame_t_0.ets: [testng] [2024-05-05 02:22:35,458] [pool-1-thread-10] Initializing /data/samples/Image SHOW/Layer&Channels.tif: [testng] [2024-05-05 02:22:36,830] [pool-1-thread-10] Initializing /data/samples/Count & Measure/Cell Multichannel-z-stack.vsi: [testng] [2024-05-05 02:22:37,959] [pool-1-thread-10] Initializing /data/samples/Deconvolution/Silver birch raw.vsi: [testng] [2024-05-05 02:22:38,633] [pool-1-thread-10] Initializing /data/alex/test.vsi: [testng] [2024-05-05 02:22:39,718] [pool-1-thread-10] Initializing /data/anda/Image_01_V76 K2 11_lung.vsi: [testng] [2024-05-05 02:22:56,334] [pool-1-thread-1] Initializing /data/samples/Count & Measure/Cell Multichannel-z-stack corr..vsi: [testng] [2024-05-05 02:22:57,352] [pool-1-thread-1] Initializing /data/samples/Process/HER2_FISH Assay.tif: [testng] [2024-05-05 02:22:58,476] [pool-1-thread-1] Initializing /data/samples/Channels/svens cells - DIC.tif: [testng] [2024-05-05 02:22:59,262] [pool-1-thread-1] Initializing /data/samples/Deconvolution/Gut section raw.vsi: [testng] [2024-05-05 02:23:00,126] [pool-1-thread-1] Initializing /data/brian/Image_28.vsi: [testng] [2024-05-05 02:23:02,229] [pool-1-thread-2] Initializing /data/gh-3822/image.jp2: [testng] [2024-05-05 02:23:06,891] [pool-1-thread-2] Initializing /data/public/evident/Image_V4.1_FL_2D.vsi: [testng] [2024-05-05 02:23:08,128] [pool-1-thread-10] Initializing /data/michelle/FC(26)-19 Gadd45b 1hr_20121011_01.vsi: [testng] [2024-05-05 02:23:13,784] [pool-1-thread-7] Initializing /data/olivier/7262 wt col.vsi: [testng] [2024-05-05 02:23:20,739] [pool-1-thread-8] Initializing /data/samples/Channels/svens cells - red.tif: [testng] [2024-05-05 02:23:21,511] [pool-1-thread-8] Initializing /data/samples/Deconvolution/_islets_40X_2_/_islets_40X_2_/stack1/frame_t_0.ets: [testng] [2024-05-05 02:23:22,666] [pool-1-thread-8] Initializing /data/anda/Image_01_V76 K2 11_lung.overview.jpg: [testng] [2024-05-05 02:23:23,370] [pool-1-thread-9] Initializing /data/david/Image_normal_skin with hair/Image_normal_skin with hair.vsi: [testng] [2024-05-05 02:23:37,819] [pool-1-thread-8] Initializing /data/samples/Measurement & ROI/Brown snake.tif: [testng] [2024-05-05 02:23:38,698] [pool-1-thread-8] Initializing /data/gh-3859/Image_Test2.vsi: [testng] [2024-05-05 02:24:06,001] [pool-1-thread-4] Initializing /data/samples/Shading Correction/Micrometer Original.tif: [testng] [2024-05-05 02:24:06,767] [pool-1-thread-4] Initializing /data/qa-11394/f1 lateral 25hpf yen4 20X timelapse.vsi: [testng] [2024-05-05 02:24:08,061] [pool-1-thread-4] Initializing /data/public/evident/Image_V4.1_BF.vsi: [testng] [2024-05-05 02:24:17,989] [pool-1-thread-9] Initializing /data/samples/Fluorescence/Dako_CISH.vsi: [testng] [2024-05-05 02:24:23,516] [pool-1-thread-9] Initializing /data/anda/Image_01_V76 K2 11_lung.thumbnail.jpg: [testng] [2024-05-05 02:24:23,780] [pool-1-thread-9] Initializing /data/olivier/26-10-2014/Image_06.vsi: [testng] [2024-05-05 02:24:35,761] [pool-1-thread-7] Initializing /data/anthony/11R1398A1.vsi: [testng] [2024-05-05 02:25:00,551] [pool-1-thread-1] Initializing /data/samples/Count & Measure/slide IHC.tif: [testng] [2024-05-05 02:25:02,684] [pool-1-thread-1] Initializing /data/public/evident/Image_V4.1_FL_3D.vsi: [testng] [2024-05-05 02:25:09,005] [pool-1-thread-8] Initializing /data/samples/Fluorescence/drehung.avi: [testng] [2024-05-05 02:25:09,978] [pool-1-thread-8] Initializing /data/samples/Shading Correction/Micrometer Background.tif: [testng] [2024-05-05 02:25:11,310] [pool-1-thread-8] Initializing /data/samples/Measurement & ROI/Cell Multichannel-M&R.tif: [testng] [2024-05-05 02:25:12,785] [pool-1-thread-8] Initializing /data/samples/Fluorescence Unmixing/HeLa_original.tif: [testng] [2024-05-05 02:25:14,999] [pool-1-thread-8] Initializing /data/melissa/artificial-vsi/Image_V4.1_BF.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 14 seconds Finished: SUCCESS