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Started by upstream project "BIOFORMATS-test-repo" build number 207 originally caused by: Started by upstream project "Trigger" build number 233 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/jenkins12085283537793388891.sh + '[' cellsens = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_32901_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] 07:39:45,606 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 07:39:45,607 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 07:39:45,607 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 07:39:45,608 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 07:39:45,608 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 07:39:45,609 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 07:39:45,609 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 07:39:45,609 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 07:39:45,609 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 07:39:45,610 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 07:39:45,610 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 07:39:45,610 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 07:39:45,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 07:39:45,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 07:39:45,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 07:39:45,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 07:39:45,788 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 07:39:45,788 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 07:39:45,788 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 07:39:45,788 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 07:39:45,788 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 07:39:45,789 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 07:39:45,790 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 181 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-02 07:39:45,798] [main] java.version = 17.0.2 [testng] 07:39:45,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 07:39:45,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:39:45,844 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-02_07-39-45.log] [testng] 07:39:45,846 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-10-02 07:39:45,848] [main] testng.directory = /data [testng] [2024-10-02 07:39:45,848] [main] testng.configDirectory = /config [testng] [2024-10-02 07:39:45,857] [main] testng.multiplier = 1.0 [testng] [2024-10-02 07:39:45,857] [main] testng.in-memory = false [testng] [2024-10-02 07:39:45,858] [main] testng.allow-missing = false [testng] [2024-10-02 07:39:45,858] [main] user.language = en [testng] [2024-10-02 07:39:45,858] [main] user.country = ${user.country} [testng] [2024-10-02 07:39:45,858] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-02 07:42:23,415] [main] ---------------------------------------- [testng] [2024-10-02 07:42:23,415] [main] Total files: 134 [testng] [2024-10-02 07:42:23,415] [main] Scan time: 157.557 s (1175 ms/file) [testng] [2024-10-02 07:42:23,415] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 72 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-02 07:43:29,650] [pool-1-thread-1] Initializing /data/david/Image_normal_skin with hair/Image_normal_skin with hair.vsi: [testng] 07:43:29,651 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 07:43:29,651 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:43:29,652 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-02_07-43-29.log] [testng] 07:43:29,652 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a8a592e - End of configuration. [testng] [2024-10-02 07:43:30,104] [pool-1-thread-12] Initializing /data/samples/Measurement & ROI/Cell Multichannel-M&R.tif: [testng] 07:43:30,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 07:43:30,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:43:30,105 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-02_07-43-30.log] [testng] 07:43:30,106 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11eb43a9 - End of configuration. [testng] [2024-10-02 07:43:31,370] [pool-1-thread-11] Initializing /data/samples/Measurement & ROI/Bandy Snake.tif: [testng] 07:43:31,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 07:43:31,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:43:31,372 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-02_07-43-31.log] [testng] 07:43:31,372 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c5ee7de - End of configuration. [testng] [2024-10-02 07:43:32,555] [pool-1-thread-10] Initializing /data/qa-18870/Image_T30.vsi: [testng] 07:43:32,555 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 07:43:32,555 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:43:32,556 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-02_07-43-32.log] [testng] 07:43:32,556 |-INFO in ch.qos.logback.core.sift.SiftProcessor@704eba6a - End of configuration. [testng] [2024-10-02 07:43:33,017] [pool-1-thread-9] Initializing /data/gh-3822/image.jp2: [testng] 07:43:33,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 07:43:33,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:43:33,018 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-02_07-43-33.log] [testng] 07:43:33,019 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b42e23b - End of configuration. [testng] [2024-10-02 07:43:34,389] [pool-1-thread-8] Initializing /data/samples/Fluorescence/Dako_CISH.vsi: [testng] 07:43:34,389 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 07:43:34,390 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:43:34,390 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-02_07-43-34.log] [testng] 07:43:34,391 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a44fae5 - End of configuration. [testng] [2024-10-02 07:43:35,100] [pool-1-thread-7] Initializing /data/samples/Fluorescence Unmixing/HeLa_GFP_only.tif: [testng] 07:43:35,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 07:43:35,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:43:35,101 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-02_07-43-35.log] [testng] 07:43:35,101 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12948c42 - End of configuration. [testng] [2024-10-02 07:43:36,104] [pool-1-thread-6] Initializing /data/olivier/7262 wt col.vsi: [testng] 07:43:36,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 07:43:36,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:43:36,105 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-02_07-43-36.log] [testng] 07:43:36,105 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c16fa05 - End of configuration. [testng] [2024-10-02 07:43:36,557] [pool-1-thread-5] Initializing /data/anda/Image_01_V76 K2 11_lung.thumbnail.jpg: [testng] 07:43:36,557 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 07:43:36,557 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:43:36,558 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-02_07-43-36.log] [testng] 07:43:36,558 |-INFO in ch.qos.logback.core.sift.SiftProcessor@397ca592 - End of configuration. [testng] [2024-10-02 07:43:36,650] [pool-1-thread-4] Initializing /data/brian/SW10082402-02_21.vsi: [testng] 07:43:36,651 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 07:43:36,651 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:43:36,651 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-02_07-43-36.log] [testng] 07:43:36,652 |-INFO in ch.qos.logback.core.sift.SiftProcessor@421c395a - End of configuration. [testng] [2024-10-02 07:43:37,221] [pool-1-thread-3] Initializing /data/samples/Fluorescence/Plant FL 100x 29 Z CI Decon2.vsi: [testng] 07:43:37,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 07:43:37,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:43:37,222 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-02_07-43-37.log] [testng] 07:43:37,222 |-INFO in ch.qos.logback.core.sift.SiftProcessor@161f0e2c - End of configuration. [testng] [2024-10-02 07:43:37,568] [pool-1-thread-2] Initializing /data/olivier/14-09-2012/Image_07.vsi: [testng] 07:43:37,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 07:43:37,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:43:37,569 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-02_07-43-37.log] [testng] 07:43:37,569 |-INFO in ch.qos.logback.core.sift.SiftProcessor@706f0996 - End of configuration. [testng] [2024-10-02 07:43:41,406] [pool-1-thread-5] Initializing /data/olivier/26-10-2014/Image_27_2.vsi: [testng] [2024-10-02 07:43:43,291] [pool-1-thread-3] Initializing /data/samples/Channels/svens cells - blue.tif: [testng] [2024-10-02 07:43:45,172] [pool-1-thread-8] Initializing /data/brian/Image_28.vsi: [testng] [2024-10-02 07:43:45,653] [pool-1-thread-11] Initializing /data/samples/Fluorescence Unmixing/HeLa_unmixed.tif: [testng] [2024-10-02 07:43:46,963] [pool-1-thread-7] Initializing /data/qa-11394/f1 lateral 25hpf yen4 20X timelapse.vsi: [testng] [2024-10-02 07:43:47,697] [pool-1-thread-12] Initializing /data/samples/Fluorescence Unmixing/HeLa_YFP_only.tif: [testng] [2024-10-02 07:43:50,191] [pool-1-thread-9] Initializing /data/olivier/26-10-2014/Image_27.vsi: [testng] [2024-10-02 07:43:54,606] [pool-1-thread-3] Initializing /data/public/evident/Image_V4.1_FL_3D.vsi: [testng] [2024-10-02 07:43:57,501] [pool-1-thread-7] Initializing /data/samples/Count & Measure/Cell Multichannel-z-stack corr..vsi: [testng] [2024-10-02 07:43:58,033] [pool-1-thread-11] Initializing /data/samples/Measurement & ROI/Intensity t series.vsi: [testng] [2024-10-02 07:43:58,743] [pool-1-thread-12] Initializing /data/gh-3822/_image_/stack1/frame_t_0.ets: [testng] [2024-10-02 07:44:03,262] [pool-1-thread-7] Initializing /data/public/evident/Image_V4.1_BF.vsi: [testng] [2024-10-02 07:44:05,360] [pool-1-thread-11] Initializing /data/qa-11039/Image_01.vsi: [testng] [2024-10-02 07:44:57,496] [pool-1-thread-12] Initializing /data/samples/Channels/Composite.vsi: [testng] [2024-10-02 07:45:01,325] [pool-1-thread-12] Initializing /data/samples/Measurement & ROI/Brown snake.tif: [testng] [2024-10-02 07:45:07,787] [pool-1-thread-12] Initializing /data/olivier/14-09-2012/Image_01.vsi: [testng] [2024-10-02 07:45:37,593] [pool-1-thread-1] Initializing /data/robert/Lung_Mite.vsi: [testng] [2024-10-02 07:45:41,261] [pool-1-thread-1] Initializing /data/samples/Deconvolution/_chroma liver 40x 8 planes_/stack1/frame_t_0.ets: [testng] [2024-10-02 07:45:47,463] [pool-1-thread-1] Initializing /data/samples/Colocalisation/Daisy_Coloc.vsi: [testng] [2024-10-02 07:45:51,951] [pool-1-thread-1] Initializing /data/gh-3859/Image_Test2.vsi: [testng] [2024-10-02 07:46:06,596] [pool-1-thread-4] Initializing /data/samples/Count & Measure/slide IHC.tif: [testng] [2024-10-02 07:46:12,724] [pool-1-thread-4] Initializing /data/melissa/SW10082402-02_21 - cy2 - cy5 copy.vsi: [testng] [2024-10-02 07:46:50,418] [pool-1-thread-6] Initializing /data/anthony/11R1398A1.vsi: [testng] [2024-10-02 07:47:21,570] [pool-1-thread-5] Initializing /data/melissa/artificial-vsi/Image_V4.1_BF.vsi: [testng] [2024-10-02 07:47:39,172] [pool-1-thread-9] Initializing /data/samples/Deconvolution/Gut section raw.vsi: [testng] [2024-10-02 07:47:44,251] [pool-1-thread-9] Initializing /data/samples/Fluorescence Unmixing/HeLa_original.tif: [testng] [2024-10-02 07:47:54,735] [pool-1-thread-9] Initializing /data/samples/Channels/svens cells - red.tif: [testng] [2024-10-02 07:47:59,075] [pool-1-thread-8] Initializing /data/samples/Count & Measure/color squares.tif: [testng] [2024-10-02 07:48:05,294] [pool-1-thread-9] Initializing /data/alex/test.vsi: [testng] [2024-10-02 07:48:12,148] [pool-1-thread-8] Initializing /data/samples/Channels/svens cells - green.tif: [testng] [2024-10-02 07:48:16,416] [pool-1-thread-9] Initializing /data/samples/Measurement & ROI/Oxyuranus_microlepidotus.tif: [testng] [2024-10-02 07:48:21,055] [pool-1-thread-8] Initializing /data/qa-29751/VSI-import-example-file.vsi: [testng] [2024-10-02 07:48:26,500] [pool-1-thread-9] Initializing /data/samples/Count & Measure/color dots.tif: [testng] [2024-10-02 07:48:28,987] [pool-1-thread-4] Initializing /data/samples/Shading Correction/Micrometer Background.tif: [testng] [2024-10-02 07:48:39,974] [pool-1-thread-4] Initializing /data/anda/Image_01_V76 K2 11_lung.vsi: [testng] [2024-10-02 07:48:40,769] [pool-1-thread-9] Initializing /data/david/smithd_20111115_1.vsi: [testng] [2024-10-02 07:49:03,119] [pool-1-thread-7] Initializing /data/olivier/Stress47_02.vsi: [testng] [2024-10-02 07:49:33,221] [pool-1-thread-3] Initializing /data/melissa/SW10082402-02_21 - 1 - GOLD copy.vsi: [testng] [2024-10-02 07:49:42,891] [pool-1-thread-4] Initializing /data/olivier/26-10-2014/Image_06.vsi: [testng] [2024-10-02 07:49:49,215] [pool-1-thread-12] Initializing /data/samples/Shading Correction/Micrometer Original.tif: [testng] [2024-10-02 07:49:58,457] [pool-1-thread-12] Initializing /data/samples/Channels/svens cells - DIC.tif: [testng] [2024-10-02 07:50:02,234] [pool-1-thread-1] Initializing /data/samples/Deconvolution/Silver birch raw.vsi: [testng] [2024-10-02 07:50:05,736] [pool-1-thread-12] Initializing /data/brian/BZ cfos1-2_05.vsi: [testng] [2024-10-02 07:50:09,309] [pool-1-thread-1] Initializing /data/samples/Image SHOW/HER2_FISH Assay.tif: [testng] [2024-10-02 07:50:18,764] [pool-1-thread-1] Initializing /data/gh-3819/H30-18-endo-sost-40x.vsi: [testng] [2024-10-02 07:50:43,907] [pool-1-thread-1] Initializing /data/samples/Process/Epithelial Cells3.tif: [testng] [2024-10-02 07:50:49,474] [pool-1-thread-1] Initializing /data/public/evident/Image_V4.1_FL_2D.vsi: [testng] [2024-10-02 07:51:50,481] [pool-1-thread-3] Initializing /data/samples/Process/HER2_FISH Assay.tif: [testng] [2024-10-02 07:52:27,933] [pool-1-thread-7] Initializing /data/olivier/Image_06.vsi: [testng] [2024-10-02 07:53:18,599] [pool-1-thread-12] Initializing /data/samples/Deconvolution/Skin 2.tif: [testng] [2024-10-02 07:53:19,352] [pool-1-thread-3] Initializing /data/alex/pN1_new.vsi: [testng] [2024-10-02 07:53:23,326] [pool-1-thread-12] Initializing /data/michelle/FC(26)-19 Gadd45b 1hr_20121011_01.vsi: [testng] [2024-10-02 07:53:30,232] [pool-1-thread-8] Initializing /data/anda/Image_01_V76 K2 11_lung.overview.jpg: [testng] [2024-10-02 07:53:44,096] [pool-1-thread-5] Initializing /data/samples/Count & Measure/Cell Multichannel-z-stack.vsi: [testng] [2024-10-02 07:53:45,392] [pool-1-thread-8] Initializing /data/olivier/small-tiles/esgTS-+;Sox21a[6]-+_30D25_09.vsi: [testng] [2024-10-02 07:53:46,529] [pool-1-thread-9] Initializing /data/samples/Deconvolution/_islets_40X_2_/_islets_40X_2_/stack1/frame_t_0.ets: [testng] [2024-10-02 07:53:47,823] [pool-1-thread-5] Initializing /data/samples/Measurement & ROI/Snake.tif: [testng] [2024-10-02 07:53:51,924] [pool-1-thread-9] Initializing /data/samples/Image SHOW/Layer&Channels.tif: [testng] [2024-10-02 07:53:53,115] [pool-1-thread-5] Initializing /data/samples/Fluorescence/drehung.avi: [testng] [2024-10-02 07:53:55,245] [pool-1-thread-5] Initializing /data/johannes/PSF_green_1.vsi: FATAL: command execution failed java.nio.channels.ClosedChannelException at org.jenkinsci.remoting.protocol.impl.ChannelApplicationLayer.onReadClosed(ChannelApplicationLayer.java:241) at org.jenkinsci.remoting.protocol.ApplicationLayer.onRecvClosed(ApplicationLayer.java:221) at org.jenkinsci.remoting.protocol.ProtocolStack$Ptr.onRecvClosed(ProtocolStack.java:825) at org.jenkinsci.remoting.protocol.FilterLayer.onRecvClosed(FilterLayer.java:289) at org.jenkinsci.remoting.protocol.impl.SSLEngineFilterLayer.onRecvClosed(SSLEngineFilterLayer.java:177) at org.jenkinsci.remoting.protocol.impl.SSLEngineFilterLayer.switchToNoSecure(SSLEngineFilterLayer.java:279) at org.jenkinsci.remoting.protocol.impl.SSLEngineFilterLayer.processWrite(SSLEngineFilterLayer.java:501) at org.jenkinsci.remoting.protocol.impl.SSLEngineFilterLayer.processQueuedWrites(SSLEngineFilterLayer.java:244) at org.jenkinsci.remoting.protocol.impl.SSLEngineFilterLayer.doSend(SSLEngineFilterLayer.java:196) at org.jenkinsci.remoting.protocol.impl.SSLEngineFilterLayer.doCloseSend(SSLEngineFilterLayer.java:209) at org.jenkinsci.remoting.protocol.ProtocolStack$Ptr.doCloseSend(ProtocolStack.java:793) at org.jenkinsci.remoting.protocol.ApplicationLayer.doCloseWrite(ApplicationLayer.java:172) at org.jenkinsci.remoting.protocol.impl.ChannelApplicationLayer$ByteBufferCommandTransport.closeWrite(ChannelApplicationLayer.java:343) at hudson.remoting.Channel.close(Channel.java:1497) at hudson.remoting.Channel.close(Channel.java:1450) at hudson.slaves.SlaveComputer.closeChannel(SlaveComputer.java:943) at hudson.slaves.SlaveComputer.kill(SlaveComputer.java:909) at hudson.model.AbstractCIBase.killComputer(AbstractCIBase.java:97) at jenkins.model.Jenkins.lambda$_cleanUpDisconnectComputers$11(Jenkins.java:3785) at hudson.model.Queue._withLock(Queue.java:1401) at hudson.model.Queue.withLock(Queue.java:1275) at jenkins.model.Jenkins._cleanUpDisconnectComputers(Jenkins.java:3781) at jenkins.model.Jenkins.cleanUp(Jenkins.java:3662) at hudson.WebAppMain.contextDestroyed(WebAppMain.java:374) at org.eclipse.jetty.server.handler.ContextHandler.callContextDestroyed(ContextHandler.java:1059) at org.eclipse.jetty.servlet.ServletContextHandler.callContextDestroyed(ServletContextHandler.java:636) at org.eclipse.jetty.server.handler.ContextHandler.contextDestroyed(ContextHandler.java:1016) at org.eclipse.jetty.servlet.ServletHandler.doStop(ServletHandler.java:306) at org.eclipse.jetty.util.component.AbstractLifeCycle.stop(AbstractLifeCycle.java:132) at org.eclipse.jetty.util.component.ContainerLifeCycle.stop(ContainerLifeCycle.java:182) at org.eclipse.jetty.util.component.ContainerLifeCycle.doStop(ContainerLifeCycle.java:205) at org.eclipse.jetty.server.handler.AbstractHandler.doStop(AbstractHandler.java:97) at org.eclipse.jetty.security.SecurityHandler.doStop(SecurityHandler.java:412) at org.eclipse.jetty.security.ConstraintSecurityHandler.doStop(ConstraintSecurityHandler.java:413) at org.eclipse.jetty.util.component.AbstractLifeCycle.stop(AbstractLifeCycle.java:132) at org.eclipse.jetty.util.component.ContainerLifeCycle.stop(ContainerLifeCycle.java:182) at org.eclipse.jetty.util.component.ContainerLifeCycle.doStop(ContainerLifeCycle.java:205) at org.eclipse.jetty.server.handler.AbstractHandler.doStop(AbstractHandler.java:97) at org.eclipse.jetty.server.session.SessionHandler.doStop(SessionHandler.java:497) at org.eclipse.jetty.util.component.AbstractLifeCycle.stop(AbstractLifeCycle.java:132) at org.eclipse.jetty.util.component.ContainerLifeCycle.stop(ContainerLifeCycle.java:182) at org.eclipse.jetty.util.component.ContainerLifeCycle.doStop(ContainerLifeCycle.java:205) at org.eclipse.jetty.server.handler.AbstractHandler.doStop(AbstractHandler.java:97) at org.eclipse.jetty.server.handler.ContextHandler.stopContext(ContextHandler.java:1039) at org.eclipse.jetty.servlet.ServletContextHandler.stopContext(ServletContextHandler.java:399) at org.eclipse.jetty.webapp.WebAppContext.stopContext(WebAppContext.java:1311) at org.eclipse.jetty.server.handler.ContextHandler.doStop(ContextHandler.java:1087) at org.eclipse.jetty.servlet.ServletContextHandler.doStop(ServletContextHandler.java:312) at org.eclipse.jetty.util.component.AbstractLifeCycle.stop(AbstractLifeCycle.java:132) at org.eclipse.jetty.util.component.ContainerLifeCycle.stop(ContainerLifeCycle.java:182) at org.eclipse.jetty.util.component.ContainerLifeCycle.doStop(ContainerLifeCycle.java:205) at org.eclipse.jetty.server.handler.AbstractHandler.doStop(AbstractHandler.java:97) at org.eclipse.jetty.server.Server.doStop(Server.java:517) at org.eclipse.jetty.util.component.AbstractLifeCycle.stop(AbstractLifeCycle.java:132) at winstone.Launcher.shutdown(Launcher.java:442) at winstone.ShutdownHook.run(ShutdownHook.java:28) Caused: java.io.IOException: Backing channel 'JNLP4-connect connection from merge-ci-docker-1.merge-ci_omero-network/172.18.0.3:45366' is disconnected. at hudson.remoting.RemoteInvocationHandler.channelOrFail(RemoteInvocationHandler.java:215) at hudson.remoting.RemoteInvocationHandler.invoke(RemoteInvocationHandler.java:285) at jdk.proxy2/jdk.proxy2.$Proxy188.isAlive(Unknown Source) at hudson.Launcher$RemoteLauncher$ProcImpl.isAlive(Launcher.java:1212) at hudson.Launcher$RemoteLauncher$ProcImpl.join(Launcher.java:1204) at hudson.tasks.CommandInterpreter.join(CommandInterpreter.java:195) at hudson.tasks.CommandInterpreter.perform(CommandInterpreter.java:145) at hudson.tasks.CommandInterpreter.perform(CommandInterpreter.java:92) at hudson.tasks.BuildStepMonitor$1.perform(BuildStepMonitor.java:20) at hudson.model.AbstractBuild$AbstractBuildExecution.perform(AbstractBuild.java:818) at hudson.model.Build$BuildExecution.build(Build.java:199) at hudson.model.Build$BuildExecution.doRun(Build.java:164) at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:526) at hudson.model.Run.execute(Run.java:1895) at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:44) at hudson.model.ResourceController.execute(ResourceController.java:101) at hudson.model.Executor.run(Executor.java:442) FATAL: Unable to delete script file /tmp/jenkins12085283537793388891.sh java.nio.channels.ClosedChannelException at org.jenkinsci.remoting.protocol.impl.ChannelApplicationLayer.onReadClosed(ChannelApplicationLayer.java:241) at org.jenkinsci.remoting.protocol.ApplicationLayer.onRecvClosed(ApplicationLayer.java:221) at org.jenkinsci.remoting.protocol.ProtocolStack$Ptr.onRecvClosed(ProtocolStack.java:825) at org.jenkinsci.remoting.protocol.FilterLayer.onRecvClosed(FilterLayer.java:289) at org.jenkinsci.remoting.protocol.impl.SSLEngineFilterLayer.onRecvClosed(SSLEngineFilterLayer.java:177) at org.jenkinsci.remoting.protocol.impl.SSLEngineFilterLayer.switchToNoSecure(SSLEngineFilterLayer.java:279) at org.jenkinsci.remoting.protocol.impl.SSLEngineFilterLayer.processWrite(SSLEngineFilterLayer.java:501) at org.jenkinsci.remoting.protocol.impl.SSLEngineFilterLayer.processQueuedWrites(SSLEngineFilterLayer.java:244) at org.jenkinsci.remoting.protocol.impl.SSLEngineFilterLayer.doSend(SSLEngineFilterLayer.java:196) at org.jenkinsci.remoting.protocol.impl.SSLEngineFilterLayer.doCloseSend(SSLEngineFilterLayer.java:209) at org.jenkinsci.remoting.protocol.ProtocolStack$Ptr.doCloseSend(ProtocolStack.java:793) at org.jenkinsci.remoting.protocol.ApplicationLayer.doCloseWrite(ApplicationLayer.java:172) at org.jenkinsci.remoting.protocol.impl.ChannelApplicationLayer$ByteBufferCommandTransport.closeWrite(ChannelApplicationLayer.java:343) at hudson.remoting.Channel.close(Channel.java:1497) at hudson.remoting.Channel.close(Channel.java:1450) at hudson.slaves.SlaveComputer.closeChannel(SlaveComputer.java:943) at hudson.slaves.SlaveComputer.kill(SlaveComputer.java:909) at hudson.model.AbstractCIBase.killComputer(AbstractCIBase.java:97) at jenkins.model.Jenkins.lambda$_cleanUpDisconnectComputers$11(Jenkins.java:3785) at hudson.model.Queue._withLock(Queue.java:1401) at hudson.model.Queue.withLock(Queue.java:1275) at jenkins.model.Jenkins._cleanUpDisconnectComputers(Jenkins.java:3781) at jenkins.model.Jenkins.cleanUp(Jenkins.java:3662) at hudson.WebAppMain.contextDestroyed(WebAppMain.java:374) at org.eclipse.jetty.server.handler.ContextHandler.callContextDestroyed(ContextHandler.java:1059) at org.eclipse.jetty.servlet.ServletContextHandler.callContextDestroyed(ServletContextHandler.java:636) at org.eclipse.jetty.server.handler.ContextHandler.contextDestroyed(ContextHandler.java:1016) at org.eclipse.jetty.servlet.ServletHandler.doStop(ServletHandler.java:306) at org.eclipse.jetty.util.component.AbstractLifeCycle.stop(AbstractLifeCycle.java:132) at org.eclipse.jetty.util.component.ContainerLifeCycle.stop(ContainerLifeCycle.java:182) at org.eclipse.jetty.util.component.ContainerLifeCycle.doStop(ContainerLifeCycle.java:205) at org.eclipse.jetty.server.handler.AbstractHandler.doStop(AbstractHandler.java:97) at org.eclipse.jetty.security.SecurityHandler.doStop(SecurityHandler.java:412) at org.eclipse.jetty.security.ConstraintSecurityHandler.doStop(ConstraintSecurityHandler.java:413) at org.eclipse.jetty.util.component.AbstractLifeCycle.stop(AbstractLifeCycle.java:132) at org.eclipse.jetty.util.component.ContainerLifeCycle.stop(ContainerLifeCycle.java:182) at org.eclipse.jetty.util.component.ContainerLifeCycle.doStop(ContainerLifeCycle.java:205) at org.eclipse.jetty.server.handler.AbstractHandler.doStop(AbstractHandler.java:97) at org.eclipse.jetty.server.session.SessionHandler.doStop(SessionHandler.java:497) at org.eclipse.jetty.util.component.AbstractLifeCycle.stop(AbstractLifeCycle.java:132) at org.eclipse.jetty.util.component.ContainerLifeCycle.stop(ContainerLifeCycle.java:182) at org.eclipse.jetty.util.component.ContainerLifeCycle.doStop(ContainerLifeCycle.java:205) at org.eclipse.jetty.server.handler.AbstractHandler.doStop(AbstractHandler.java:97) at org.eclipse.jetty.server.handler.ContextHandler.stopContext(ContextHandler.java:1039) at org.eclipse.jetty.servlet.ServletContextHandler.stopContext(ServletContextHandler.java:399) at org.eclipse.jetty.webapp.WebAppContext.stopContext(WebAppContext.java:1311) at org.eclipse.jetty.server.handler.ContextHandler.doStop(ContextHandler.java:1087) at org.eclipse.jetty.servlet.ServletContextHandler.doStop(ServletContextHandler.java:312) at org.eclipse.jetty.util.component.AbstractLifeCycle.stop(AbstractLifeCycle.java:132) at org.eclipse.jetty.util.component.ContainerLifeCycle.stop(ContainerLifeCycle.java:182) at org.eclipse.jetty.util.component.ContainerLifeCycle.doStop(ContainerLifeCycle.java:205) at org.eclipse.jetty.server.handler.AbstractHandler.doStop(AbstractHandler.java:97) at org.eclipse.jetty.server.Server.doStop(Server.java:517) at org.eclipse.jetty.util.component.AbstractLifeCycle.stop(AbstractLifeCycle.java:132) at winstone.Launcher.shutdown(Launcher.java:442) at winstone.ShutdownHook.run(ShutdownHook.java:28) Caused: hudson.remoting.ChannelClosedException: Channel "hudson.remoting.Channel@d0b6132:JNLP4-connect connection from merge-ci-docker-1.merge-ci_omero-network/172.18.0.3:45366": Remote call on JNLP4-connect connection from merge-ci-docker-1.merge-ci_omero-network/172.18.0.3:45366 failed. The channel is closing down or has closed down at hudson.remoting.Channel.call(Channel.java:996) at hudson.FilePath.act(FilePath.java:1230) at hudson.FilePath.act(FilePath.java:1219) at hudson.FilePath.delete(FilePath.java:1766) at hudson.tasks.CommandInterpreter.perform(CommandInterpreter.java:163) at hudson.tasks.CommandInterpreter.perform(CommandInterpreter.java:92) at hudson.tasks.BuildStepMonitor$1.perform(BuildStepMonitor.java:20) at hudson.model.AbstractBuild$AbstractBuildExecution.perform(AbstractBuild.java:818) at hudson.model.Build$BuildExecution.build(Build.java:199) at hudson.model.Build$BuildExecution.doRun(Build.java:164) at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:526) at hudson.model.Run.execute(Run.java:1895) at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:44) at hudson.model.ResourceController.execute(ResourceController.java:101) at hudson.model.Executor.run(Executor.java:442) Build step 'Execute shell' marked build as failure Finished: FAILURE