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Started by upstream project "BIOFORMATS-test-repo" build number 288 originally caused by: Started by upstream project "Trigger" build number 307 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins8782990068752323419.sh + '[' bmp = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_45446_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings 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] 00:34:14,748 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:34:14,749 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 00:34:14,749 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:34:14,750 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:34:14,751 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:34:14,751 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:34:14,751 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:34:14,751 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:34:14,752 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:34:14,752 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:34:14,753 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:34:14,753 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:34:14,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:34:14,918 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:34:14,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:34:14,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:34:14,952 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:34:14,952 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:34:14,952 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:34:14,953 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:34:14,953 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 00:34:14,954 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 00:34:14,954 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 202 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-12 00:34:14,963] [main] java.version = 21 [testng] 00:34:14,966 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:34:14,966 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:15,009 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-12_00-34-14.log] [testng] 00:34:15,010 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-12-12 00:34:15,012] [main] testng.directory = /data [testng] [2024-12-12 00:34:15,012] [main] testng.configDirectory = /config [testng] [2024-12-12 00:34:15,022] [main] testng.multiplier = 1.0 [testng] [2024-12-12 00:34:15,023] [main] testng.in-memory = false [testng] [2024-12-12 00:34:15,023] [main] testng.allow-missing = false [testng] [2024-12-12 00:34:15,023] [main] user.language = en [testng] [2024-12-12 00:34:15,023] [main] user.country = ${user.country} [testng] [2024-12-12 00:34:15,023] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-12 00:34:16,023] [main] ---------------------------------------- [testng] [2024-12-12 00:34:16,023] [main] Total files: 31 [testng] [2024-12-12 00:34:16,023] [main] Scan time: 1.0 s (32 ms/file) [testng] [2024-12-12 00:34:16,023] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 31 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-12 00:34:25,351] [pool-1-thread-1] Initializing /data/dennis/kidney_TFl_One.bmp: [testng] 00:34:25,352 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:34:25,353 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:25,355 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-12_00-34-25.log] [testng] 00:34:25,355 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4388387a - End of configuration. [testng] [2024-12-12 00:34:25,518] [pool-1-thread-12] Initializing /data/brian/images/23srp5dksub.bmp: [testng] 00:34:25,519 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:34:25,519 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:25,520 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-12_00-34-25.log] [testng] 00:34:25,520 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40ad89ef - End of configuration. [testng] [2024-12-12 00:34:25,684] [pool-1-thread-11] Initializing /data/qa-4538/22577136_Figure 2_A_ATF6 (GST)_13572.bmp: [testng] 00:34:25,684 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:34:25,684 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:25,685 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-12_00-34-25.log] [testng] 00:34:25,685 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31b0fa79 - End of configuration. [testng] [2024-12-12 00:34:25,977] [pool-1-thread-10] Initializing /data/dennis/kidney_TFl_Four.bmp: [testng] 00:34:25,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:34:25,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:25,978 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-12_00-34-25.log] [testng] 00:34:25,979 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74e2ac77 - End of configuration. [testng] [2024-12-12 00:34:26,144] [pool-1-thread-9] Initializing /data/big-images/6kx6k.bmp: [testng] 00:34:26,145 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:34:26,145 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:26,145 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-12_00-34-26.log] [testng] 00:34:26,146 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77863339 - End of configuration. [testng] [2024-12-12 00:34:26,307] [pool-1-thread-8] Initializing /data/dennis/kidney_TFl_Seven.bmp: [testng] 00:34:26,307 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:34:26,307 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:26,308 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-12_00-34-26.log] [testng] 00:34:26,308 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63156615 - End of configuration. [testng] [2024-12-12 00:34:26,533] [pool-1-thread-7] Initializing /data/brian/images/kidney_TFl_1_greyscale.bmp: [testng] 00:34:26,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:34:26,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:26,533 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-12_00-34-26.log] [testng] 00:34:26,534 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75bdbd1b - End of configuration. [testng] [2024-12-12 00:34:26,775] [pool-1-thread-6] Initializing /data/dennis/kidney_TFl_Two.bmp: [testng] 00:34:26,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:34:26,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:26,776 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-12_00-34-26.log] [testng] 00:34:26,776 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ebbb5f8 - End of configuration. [testng] [2024-12-12 00:34:26,956] [pool-1-thread-5] Initializing /data/dennis/kidney_TFl_Eight.bmp: [testng] 00:34:26,956 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:34:26,956 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:26,957 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-12_00-34-26.log] [testng] 00:34:26,958 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3de25fa - End of configuration. [testng] [2024-12-12 00:34:27,137] [pool-1-thread-4] Initializing /data/frank/cell_mask_error.bmp: [testng] 00:34:27,138 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:34:27,138 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:27,138 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-12_00-34-27.log] [testng] 00:34:27,139 |-INFO in ch.qos.logback.core.sift.SiftProcessor@377b05 - End of configuration. [testng] [2024-12-12 00:34:27,317] [pool-1-thread-3] Initializing /data/curtis/image5.bmp: [testng] 00:34:27,317 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:34:27,317 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:27,318 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-12_00-34-27.log] [testng] 00:34:27,319 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23c89263 - End of configuration. [testng] [2024-12-12 00:34:27,496] [pool-1-thread-2] Initializing /data/curtis/image4.bmp: [testng] 00:34:27,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:34:27,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:27,497 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-12_00-34-27.log] [testng] 00:34:27,498 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7cd27bf9 - End of configuration. [testng] [2024-12-12 00:34:32,332] [pool-1-thread-2] Initializing /data/dennis/kidney_TFl_Five.bmp: [testng] [2024-12-12 00:34:32,502] [pool-1-thread-3] Initializing /data/brian/images/kidney_TFl_1.bmp: [testng] [2024-12-12 00:34:32,662] [pool-1-thread-7] Initializing /data/dennis/kidney_TFl_Six.bmp: [testng] [2024-12-12 00:34:32,830] [pool-1-thread-8] Initializing /data/brian/images/DMSOHigh_001.bmp: [testng] [2024-12-12 00:34:32,997] [pool-1-thread-1] Initializing /data/bk/ch_00.bmp: [testng] [2024-12-12 00:34:33,170] [pool-1-thread-5] Initializing /data/brian/images/raw_a_rg.tiff: [testng] [2024-12-12 00:34:35,124] [pool-1-thread-4] Initializing /data/curtis/image3.bmp: [testng] [2024-12-12 00:34:35,306] [pool-1-thread-6] Initializing /data/big-images/8kx8k.bmp: [testng] [2024-12-12 00:34:35,464] [pool-1-thread-10] Initializing /data/stephane/holo0908.bmp: [testng] [2024-12-12 00:34:35,608] [pool-1-thread-12] Initializing /data/big-images/8kx8k-grey.bmp: [testng] [2024-12-12 00:34:35,772] [pool-1-thread-11] Initializing /data/brian/images/raw_a.bmp: [testng] [2024-12-12 00:34:39,243] [pool-1-thread-4] Initializing /data/dennis/kidney_TFl_Three.bmp: [testng] [2024-12-12 00:34:39,396] [pool-1-thread-2] Initializing /data/curtis/image1.bmp: [testng] [2024-12-12 00:34:39,596] [pool-1-thread-11] Initializing /data/curtis/image2.bmp: [testng] [2024-12-12 00:34:39,765] [pool-1-thread-7] Initializing /data/bk/100427RBTLPC_FD3__A___5_T_001_ch_00_image_00025_Z_001.bmp: [testng] [2024-12-12 00:34:39,949] [pool-1-thread-3] Initializing /data/big-images/6kx6k-grey.bmp: [testng] [2024-12-12 00:34:40,109] [pool-1-thread-8] Initializing /data/brian/images/raw_a_rg.bmp: [testng] [2024-12-12 00:34:40,294] [pool-1-thread-10] Initializing /data/dennis/kidney_TFl_Nine.bmp: [testng] [2024-12-12 00:34:40,518] [pool-1-thread-1] Initializing /data/ticket-12971/foo.bmp: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1643, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 47 seconds Finished: SUCCESS