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@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins13238867805600978292.sh + '[' ome-tiff = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_32841_merge_ci -v /uod/idr/repos/curated/ome-tiff:/data -v /uod/idr-scratch/merge-ci/curated/ome-tiff:/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] 02:33:22,429 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:33:22,430 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 02:33:22,430 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:33:22,431 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:33:22,431 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:33:22,432 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:33:22,432 |-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] 02:33:22,432 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:33:22,432 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:33:22,433 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:33:22,433 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:33:22,433 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:33:22,583 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:33:22,583 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:33:22,603 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:33:22,604 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:33:22,609 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:33:22,609 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:33:22,609 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:33:22,610 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:33:22,610 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 02:33:22,610 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 02:33:22,610 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 178 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-02 02:33:22,618] [main] java.version = 17.0.2 [testng] 02:33:22,623 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:33:22,623 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:33:22,661 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-02_02-33-22.log] [testng] 02:33:22,662 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-10-02 02:33:22,664] [main] testng.directory = /data [testng] [2024-10-02 02:33:22,664] [main] testng.configDirectory = /config [testng] [2024-10-02 02:33:22,673] [main] testng.multiplier = 1.0 [testng] [2024-10-02 02:33:22,673] [main] testng.in-memory = false [testng] [2024-10-02 02:33:22,674] [main] testng.allow-missing = false [testng] [2024-10-02 02:33:22,674] [main] user.language = en [testng] [2024-10-02 02:33:22,674] [main] user.country = ${user.country} [testng] [2024-10-02 02:33:22,674] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-02 02:41:45,498] [main] ---------------------------------------- [testng] [2024-10-02 02:41:45,498] [main] Total files: 4771 [testng] [2024-10-02 02:41:45,498] [main] Scan time: 502.824 s (105 ms/file) [testng] [2024-10-02 02:41:45,498] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 1455 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-02 05:19:31,711] [pool-1-thread-1] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y00/image--L09--S00--U00--V00--J00--X00--Y00--T09--Z00--C00.ome.tif: [testng] 05:19:31,712 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 05:19:31,712 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:19:31,714 |-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_05-19-31.log] [testng] 05:19:31,714 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7799fd09 - End of configuration. [testng] [2024-10-02 05:19:41,437] [pool-1-thread-12] Initializing /data/pam/try-09242010-1031-049/try-09242010-1031-049.xml: [testng] 05:19:41,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 05:19:41,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:19:41,438 |-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_05-19-41.log] [testng] 05:19:41,438 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7782a48c - End of configuration. [testng] [2024-10-02 05:19:47,365] [pool-1-thread-11] Initializing /data/andor/iQMM_FURA_TIME180_WAVELENGTH0_0.ome.tif: [testng] 05:19:47,365 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 05:19:47,365 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:19:47,366 |-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_05-19-47.log] [testng] 05:19:47,366 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ef40e82 - End of configuration. [testng] [2024-10-02 05:19:51,814] [pool-1-thread-10] Initializing /data/andor/iQMM_FURA_TIME105_WAVELENGTH0_0.ome.tif: [testng] 05:19:51,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 05:19:51,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:19:51,815 |-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_05-19-51.log] [testng] 05:19:51,816 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4cbb06d8 - End of configuration. [testng] [2024-10-02 05:19:55,626] [pool-1-thread-9] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X04--Y01/image--L12--S00--U00--V00--J00--X04--Y01--T12--Z00--C00.ome.tif: [testng] 05:19:55,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 05:19:55,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:19:55,626 |-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_05-19-55.log] [testng] 05:19:55,627 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7683d1d9 - End of configuration. [testng] [2024-10-02 05:19:58,338] [pool-1-thread-8] Initializing /data/chris/Fig6/Fig 6A.ome.tiff: [testng] 05:19:58,338 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 05:19:58,338 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:19:58,339 |-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_05-19-58.log] [testng] 05:19:58,339 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19de1aa4 - End of configuration. [testng] [2024-10-02 05:20:01,961] [pool-1-thread-7] Initializing /data/public/2007-06/Iron-Plate.ome.tiff: [testng] 05:20:01,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 05:20:01,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:20:01,962 |-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_05-20-01.log] [testng] 05:20:01,962 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46357753 - End of configuration. [testng] [2024-10-02 05:20:05,951] [pool-1-thread-6] Initializing /data/oliver/DIV0Ctrl-2_1.tif: [testng] 05:20:05,951 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 05:20:05,951 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:20:05,952 |-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_05-20-05.log] [testng] 05:20:05,952 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f1bf22a - End of configuration. [testng] [2024-10-02 05:20:10,085] [pool-1-thread-5] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X01--Y02/image--L13--S00--U00--V00--J00--X01--Y02--T13--Z00--C00.ome.tif: [testng] 05:20:10,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 05:20:10,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:20:10,086 |-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_05-20-10.log] [testng] 05:20:10,086 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58d2c6b6 - End of configuration. [testng] [2024-10-02 05:20:15,067] [pool-1-thread-4] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X05--Y00/image--L05--S00--U00--V00--J00--X05--Y00--T05--Z00--C00.ome.tif: [testng] 05:20:15,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 05:20:15,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:20:15,068 |-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_05-20-15.log] [testng] 05:20:15,071 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40f65c9f - End of configuration. [testng] [2024-10-02 05:20:18,764] [pool-1-thread-3] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y06/image--L11--S00--U00--V00--J00--X02--Y06--T11--Z00--C00.ome.tif: [testng] 05:20:18,764 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 05:20:18,764 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:20:18,764 |-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_05-20-18.log] [testng] 05:20:18,765 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31011e57 - End of configuration. [testng] [2024-10-02 05:20:22,858] [pool-1-thread-2] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y00/image--L03--S00--U00--V00--J00--X03--Y00--T03--Z00--C00.ome.tif: [testng] 05:20:22,858 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 05:20:22,858 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:20:22,859 |-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_05-20-22.log] [testng] 05:20:22,859 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54d1f383 - End of configuration. [testng] [2024-10-02 05:20:43,841] [pool-1-thread-8] Initializing /data/andor/iQMM_FURA_TIME70_WAVELENGTH1_0.ome.tif: [testng] [2024-10-02 05:20:45,850] [pool-1-thread-7] Initializing /data/andor/iQMM_FURA_TIME192_WAVELENGTH0_0.ome.tif: [testng] [2024-10-02 05:20:47,574] [pool-1-thread-6] Initializing /data/public/2012-06/bioformats-artificial/single-channel.ome.tif: [testng] [2024-10-02 05:20:57,063] [pool-1-thread-4] Initializing /data/tubhiswtTEST/time2/tubhiswt_C1_TP1.ome.tif: [testng] [2024-10-02 05:22:07,696] [pool-1-thread-9] Initializing /data/andor/iQMM_FURA_TIME158_WAVELENGTH1_0.ome.tif: [testng] [2024-10-02 05:22:10,990] [pool-1-thread-2] Initializing /data/ruben/experiment--2009_10_27_15_43_34/slide--S00/chamber--U00--V00/field--X02--Y00/image--L00--S00--U00--V00--J00--X02--Y00--T00--Z00--C00.ome.tif: [testng] [2024-10-02 05:22:13,926] [pool-1-thread-5] Initializing /data/andor/iQMM_FURA_TIME151_WAVELENGTH1_0.ome.tif: [testng] [2024-10-02 05:22:16,358] [pool-1-thread-3] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X06--Y04/image--L13--S00--U00--V00--J00--X06--Y04--T13--Z00--C00.ome.tif: [testng] [2024-10-02 05:22:19,583] [pool-1-thread-1] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X06--Y04/image--L03--S00--U00--V00--J00--X06--Y04--T03--Z00--C00.ome.tif: [testng] [2024-10-02 05:22:21,688] [pool-1-thread-10] Initializing /data/andor/iQMM_FURA_TIME107_WAVELENGTH1_0.ome.tif: [testng] [2024-10-02 05:22:24,120] [pool-1-thread-11] Initializing /data/andor/iQMM_FURA_TIME185_WAVELENGTH1_0.ome.tif: [testng] [2024-10-02 05:22:35,303] [pool-1-thread-12] Initializing /data/andor/iQMM_FURA_TIME184_WAVELENGTH1_0.ome.tif: [testng] [2024-10-02 05:22:37,545] [pool-1-thread-8] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y03/image--L03--S00--U00--V00--J00--X03--Y03--T03--Z00--C00.ome.tif: [testng] [2024-10-02 05:22:39,605] [pool-1-thread-7] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y02/image--L02--S00--U00--V00--J00--X00--Y02--T02--Z00--C00.ome.tif: [testng] [2024-10-02 05:22:41,729] [pool-1-thread-6] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X05--Y04/image--L11--S00--U00--V00--J00--X05--Y04--T11--Z00--C00.ome.tif: [testng] [2024-10-02 05:22:51,677] [pool-1-thread-3] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y00/image--L00--S00--U00--V00--J00--X03--Y00--T00--Z00--C00.ome.tif: [testng] [2024-10-02 05:22:53,662] [pool-1-thread-1] Initializing /data/andor/iQMM_FURA_TIME187_WAVELENGTH1_0.ome.tif: [testng] [2024-10-02 05:22:55,788] [pool-1-thread-2] Initializing /data/public/2008-02/single-channel.ome.tif: [testng] [2024-10-02 05:22:58,559] [pool-1-thread-10] Initializing 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Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X05--Y00/image--L09--S00--U00--V00--J00--X05--Y00--T09--Z00--C00.ome.tif: [testng] [2024-10-02 07:12:06,518] [pool-1-thread-5] Initializing /data/public/2008-09/multi-pixel-default.ome.tiff: [testng] [2024-10-02 07:12:07,964] [pool-1-thread-11] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X01--Y00/image--L00--S00--U00--V00--J00--X01--Y00--T00--Z00--C00.ome.tif: [testng] [2024-10-02 07:12:09,227] [pool-1-thread-4] Initializing /data/andor/iQMM_FURA_TIME50_WAVELENGTH0_0.ome.tif: [testng] [2024-10-02 07:12:10,585] [pool-1-thread-12] Initializing /data/public/2016-06/tubhiswt-4D/tubhiswt_C0_TP0.ome.tif: [testng] [2024-10-02 07:12:39,233] [pool-1-thread-1] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X00--Y06/image--L09--S00--U00--V00--J00--X00--Y06--T09--Z00--C00.ome.tif: [testng] [2024-10-02 07:12:44,332] [pool-1-thread-5] Initializing /data/chris/Fig3/Fig 3C.ome.tiff: [testng] [2024-10-02 07:12:46,551] [pool-1-thread-11] Initializing /data/chris/Video1_SGMCA.ome.tiff: [testng] [2024-10-02 07:12:49,722] [pool-1-thread-4] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X01--Y05/image--L09--S00--U00--V00--J00--X01--Y05--T09--Z00--C00.ome.tif: [testng] [2024-10-02 07:12:52,260] [pool-1-thread-1] Initializing /data/andor/iQMM_FURA_TIME195_WAVELENGTH0_0.ome.tif: [testng] [2024-10-02 07:12:54,499] [pool-1-thread-5] Initializing /data/public/2013-06/bioformats-artificial/z-series.ome.tif: [testng] [2024-10-02 07:12:57,523] [pool-1-thread-11] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X02--Y02/image--L00--S00--U00--V00--J00--X02--Y02--T00--Z00--C00.ome.tif: [testng] [2024-10-02 07:13:00,161] [pool-1-thread-4] Initializing /data/chris/Fig4/Fig 4A.ome.tiff: [testng] [2024-10-02 07:13:03,155] [pool-1-thread-5] Initializing /data/curtis/z-series.ome.tif: [testng] [2024-10-02 07:13:06,858] [pool-1-thread-1] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y05/image--L14--S00--U00--V00--J00--X03--Y05--T14--Z00--C00.ome.tif: [testng] [2024-10-02 07:13:09,050] [pool-1-thread-11] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X06--Y05/image--L06--S00--U00--V00--J00--X06--Y05--T06--Z00--C00.ome.tif: [testng] [2024-10-02 07:13:10,329] [pool-1-thread-4] Initializing /data/andor/iQMM_FURA_TIME129_WAVELENGTH1_0.ome.tif: [testng] [2024-10-02 07:13:12,047] [pool-1-thread-5] Initializing /data/ruben/experiment--2009_10_27_15_59_00/slide--S00/chamber--U00--V00/field--X03--Y02/image--L14--S00--U00--V00--J00--X03--Y02--T14--Z00--C00.ome.tif: [testng] [2024-10-02 07:13:17,880] [pool-1-thread-1] Initializing /data/andor/iQMM_FURA_TIME178_WAVELENGTH1_0.ome.tif: [testng] [2024-10-02 07:13:21,531] [pool-1-thread-11] Initializing /data/andor/iQMM_FURA_TIME102_WAVELENGTH0_0.ome.tif: [testng] [2024-10-02 07:13:24,031] [pool-1-thread-5] Initializing /data/glen/OMETiff Slidebook donotopen/Capture 2 - Position 1_XY1306537975_Z00_T001_C1.tiff: [testng] [2024-10-02 07:13:26,192] [pool-1-thread-4] Initializing /data/chris/Fig3/Fig 3A.ome.tiff: [testng] [2024-10-02 07:13:34,740] [pool-1-thread-4] Initializing /data/ruben/experiment--2009_10_27_15_43_34/slide--S00/chamber--U00--V00/field--X00--Y01/image--L00--S00--U00--V00--J00--X00--Y01--T00--Z00--C00.ome.tif: [testng] [2024-10-02 07:13:36,096] [pool-1-thread-1] Initializing /data/andor/iQMM_FURA_TIME98_WAVELENGTH1_0.ome.tif: [testng] [2024-10-02 07:13:37,517] [pool-1-thread-5] Initializing /data/public/2009-09/one-screen-one-plate-four-wells.ome.tiff: 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$AbstractBuildExecution.run(AbstractBuild.java:526) at hudson.model.Run.execute(Run.java:1895) at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:44) at hudson.model.ResourceController.execute(ResourceController.java:101) at hudson.model.Executor.run(Executor.java:442) FATAL: Unable to delete script file /tmp/jenkins13238867805600978292.sh java.nio.channels.ClosedChannelException at org.jenkinsci.remoting.protocol.impl.ChannelApplicationLayer.onReadClosed(ChannelApplicationLayer.java:241) at org.jenkinsci.remoting.protocol.ApplicationLayer.onRecvClosed(ApplicationLayer.java:221) at org.jenkinsci.remoting.protocol.ProtocolStack$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