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