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Started by upstream project "BIOFORMATS-test-repo" build number 109 originally caused by: Started by upstream project "Trigger" build number 122 originally caused by: Started by user devspace 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/jenkins2129311984373846324.sh + '[' bmp = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_16890_merge_ci -v /uod/idr/repos/curated/bmp:/data -v /uod/idr-scratch/merge-ci/curated/bmp:/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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 12:12:08,391 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 12:12:08,393 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 12:12:08,393 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:12:08,394 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:12:08,395 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 12:12:08,395 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 12:12:08,395 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 12:12:08,395 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:12:08,396 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:12:08,396 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 12:12:08,397 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 12:12:08,397 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 12:12:08,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 12:12:08,588 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 12:12:08,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 12:12:08,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 12:12:08,620 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 12:12:08,620 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 12:12:08,620 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 12:12:08,621 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 12:12:08,621 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 12:12:08,622 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 12:12:08,622 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 226 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-02 12:12:08,632] [main] java.version = 11.0.16 [testng] 12:12:08,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 12:12:08,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:12:08,683 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-02_12-12-08.log] [testng] 12:12:08,685 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-07-02 12:12:08,688] [main] testng.directory = /data [testng] [2024-07-02 12:12:08,688] [main] testng.configDirectory = /config [testng] [2024-07-02 12:12:08,699] [main] testng.multiplier = 1.0 [testng] [2024-07-02 12:12:08,701] [main] testng.in-memory = false [testng] [2024-07-02 12:12:08,701] [main] testng.allow-missing = false [testng] [2024-07-02 12:12:08,701] [main] user.language = en [testng] [2024-07-02 12:12:08,701] [main] user.country = ${user.country} [testng] [2024-07-02 12:12:08,701] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-02 12:12:09,226] [main] ---------------------------------------- [testng] [2024-07-02 12:12:09,226] [main] Total files: 31 [testng] [2024-07-02 12:12:09,226] [main] Scan time: 0.524 s (16 ms/file) [testng] [2024-07-02 12:12:09,226] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 31 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-02 12:12:10,741] [pool-1-thread-1] Initializing /data/curtis/image2.bmp: [testng] 12:12:10,742 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 12:12:10,742 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:12:10,744 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-02_12-12-10.log] [testng] 12:12:10,744 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b695aca - End of configuration. [testng] [2024-07-02 12:12:10,767] [pool-1-thread-12] Initializing /data/brian/images/DMSOHigh_001.bmp: [testng] 12:12:10,768 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 12:12:10,768 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:12:10,770 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-02_12-12-10.log] [testng] 12:12:10,771 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b8d656d - End of configuration. [testng] [2024-07-02 12:12:10,786] [pool-1-thread-11] Initializing /data/bk/ch_00.bmp: [testng] 12:12:10,786 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 12:12:10,786 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:12:10,787 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-02_12-12-10.log] [testng] 12:12:10,788 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74e2ac77 - End of configuration. [testng] [2024-07-02 12:12:10,801] [pool-1-thread-10] Initializing /data/ticket-12971/foo.bmp: [testng] 12:12:10,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 12:12:10,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:12:10,802 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-02_12-12-10.log] [testng] 12:12:10,803 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77863339 - End of configuration. [testng] [2024-07-02 12:12:10,812] [pool-1-thread-9] Initializing /data/dennis/kidney_TFl_Three.bmp: [testng] 12:12:10,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 12:12:10,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:12:10,814 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-02_12-12-10.log] [testng] 12:12:10,814 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63156615 - End of configuration. [testng] [2024-07-02 12:12:10,824] [pool-1-thread-8] Initializing /data/big-images/6kx6k.bmp: [testng] 12:12:10,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 12:12:10,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:12:10,825 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-02_12-12-10.log] [testng] 12:12:10,825 |-INFO in ch.qos.logback.core.sift.SiftProcessor@377b05 - End of configuration. [testng] [2024-07-02 12:12:10,837] [pool-1-thread-7] Initializing /data/curtis/image1.bmp: [testng] 12:12:10,837 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 12:12:10,837 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:12:10,838 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-02_12-12-10.log] [testng] 12:12:10,839 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23c89263 - End of configuration. [testng] [2024-07-02 12:12:10,862] [pool-1-thread-6] Initializing /data/brian/images/kidney_TFl_1.bmp: [testng] 12:12:10,863 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 12:12:10,863 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:12:10,864 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-02_12-12-10.log] [testng] 12:12:10,864 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7cd27bf9 - End of configuration. [testng] [2024-07-02 12:12:10,879] [pool-1-thread-5] Initializing /data/dennis/kidney_TFl_Two.bmp: [testng] 12:12:10,879 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 12:12:10,880 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:12:10,880 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-02_12-12-10.log] [testng] 12:12:10,881 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f97c453 - End of configuration. [testng] [2024-07-02 12:12:10,903] [pool-1-thread-4] Initializing /data/curtis/image3.bmp: [testng] 12:12:10,903 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 12:12:10,903 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:12:10,904 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-02_12-12-10.log] [testng] 12:12:10,904 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52c0ab2e - End of configuration. [testng] [2024-07-02 12:12:10,910] [pool-1-thread-3] Initializing /data/brian/images/raw_a_rg.tiff: [testng] 12:12:10,910 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 12:12:10,910 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:12:10,911 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-02_12-12-10.log] [testng] 12:12:10,911 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e25aff7 - End of configuration. [testng] [2024-07-02 12:12:10,949] [pool-1-thread-2] Initializing /data/dennis/kidney_TFl_Four.bmp: [testng] 12:12:10,949 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 12:12:10,949 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:12:10,950 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-02_12-12-10.log] [testng] 12:12:10,950 |-INFO in ch.qos.logback.core.sift.SiftProcessor@567e122b - End of configuration. [testng] [2024-07-02 12:12:12,638] [pool-1-thread-10] Initializing /data/dennis/kidney_TFl_Seven.bmp: [testng] [2024-07-02 12:12:12,687] [pool-1-thread-7] Initializing /data/brian/images/raw_a_rg.bmp: [testng] [2024-07-02 12:12:12,695] [pool-1-thread-4] Initializing /data/dennis/kidney_TFl_One.bmp: [testng] [2024-07-02 12:12:12,702] [pool-1-thread-1] Initializing /data/curtis/image5.bmp: [testng] [2024-07-02 12:12:12,706] [pool-1-thread-6] Initializing /data/dennis/kidney_TFl_Five.bmp: [testng] [2024-07-02 12:12:12,714] [pool-1-thread-5] Initializing /data/qa-4538/22577136_Figure 2_A_ATF6 (GST)_13572.bmp: [testng] [2024-07-02 12:12:12,722] [pool-1-thread-9] Initializing /data/dennis/kidney_TFl_Six.bmp: [testng] [2024-07-02 12:12:12,729] [pool-1-thread-2] Initializing /data/stephane/holo0908.bmp: [testng] [2024-07-02 12:12:12,736] [pool-1-thread-12] Initializing /data/frank/cell_mask_error.bmp: [testng] [2024-07-02 12:12:12,743] [pool-1-thread-3] Initializing /data/big-images/8kx8k-grey.bmp: [testng] [2024-07-02 12:12:13,643] [pool-1-thread-1] Initializing /data/dennis/kidney_TFl_Nine.bmp: [testng] [2024-07-02 12:12:13,651] [pool-1-thread-11] Initializing /data/bk/100427RBTLPC_FD3__A___5_T_001_ch_00_image_00025_Z_001.bmp: [testng] [2024-07-02 12:12:13,871] [pool-1-thread-7] Initializing /data/brian/images/kidney_TFl_1_greyscale.bmp: [testng] [2024-07-02 12:12:13,909] [pool-1-thread-9] Initializing /data/curtis/image4.bmp: [testng] [2024-07-02 12:12:13,913] [pool-1-thread-10] Initializing /data/big-images/8kx8k.bmp: [testng] [2024-07-02 12:12:13,974] [pool-1-thread-6] Initializing /data/brian/images/raw_a.bmp: [testng] [2024-07-02 12:12:13,984] [pool-1-thread-4] Initializing /data/big-images/6kx6k-grey.bmp: [testng] [2024-07-02 12:12:13,990] [pool-1-thread-12] Initializing /data/brian/images/23srp5dksub.bmp: [testng] [2024-07-02 12:12:14,051] [pool-1-thread-1] Initializing /data/dennis/kidney_TFl_Eight.bmp: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1643, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 34 seconds Finished: SUCCESS