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Started by upstream project "BIOFORMATS-test-repo" build number 263 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins5383806699426329854.sh + '[' bmp = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_41473_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 15:34:07,878 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 15:34:07,879 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 15:34:07,879 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 15:34:07,880 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 15:34:07,880 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 15:34:07,881 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 15:34:07,881 |-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] 15:34:07,881 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 15:34:07,882 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 15:34:07,882 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 15:34:07,883 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 15:34:07,883 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 15:34:08,040 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 15:34:08,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 15:34:08,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 15:34:08,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 15:34:08,071 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 15:34:08,071 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 15:34:08,071 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 15:34:08,072 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 15:34:08,072 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 15:34:08,073 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 15:34:08,073 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 191 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-21 15:34:08,081] [main] java.version = 21 [testng] 15:34:08,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 15:34:08,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:34:08,124 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-21_15-34-08.log] [testng] 15:34:08,126 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-11-21 15:34:08,127] [main] testng.directory = /data [testng] [2024-11-21 15:34:08,127] [main] testng.configDirectory = /config [testng] [2024-11-21 15:34:08,136] [main] testng.multiplier = 1.0 [testng] [2024-11-21 15:34:08,136] [main] testng.in-memory = false [testng] [2024-11-21 15:34:08,137] [main] testng.allow-missing = false [testng] [2024-11-21 15:34:08,137] [main] user.language = en [testng] [2024-11-21 15:34:08,137] [main] user.country = ${user.country} [testng] [2024-11-21 15:34:08,137] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-21 15:34:09,173] [main] ---------------------------------------- [testng] [2024-11-21 15:34:09,174] [main] Total files: 31 [testng] [2024-11-21 15:34:09,174] [main] Scan time: 1.036 s (33 ms/file) [testng] [2024-11-21 15:34:09,174] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 31 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-21 15:34:17,298] [pool-1-thread-1] Initializing /data/dennis/kidney_TFl_One.bmp: [testng] 15:34:17,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 15:34:17,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:34:17,301 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-21_15-34-17.log] [testng] 15:34:17,302 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77cf7a3f - End of configuration. [testng] [2024-11-21 15:34:17,425] [pool-1-thread-12] Initializing /data/brian/images/23srp5dksub.bmp: [testng] 15:34:17,425 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 15:34:17,426 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:34:17,426 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-21_15-34-17.log] [testng] 15:34:17,427 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f8b5644 - End of configuration. [testng] [2024-11-21 15:34:17,544] [pool-1-thread-11] Initializing /data/qa-4538/22577136_Figure 2_A_ATF6 (GST)_13572.bmp: [testng] 15:34:17,544 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 15:34:17,544 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:34:17,545 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-21_15-34-17.log] [testng] 15:34:17,545 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52b03eff - End of configuration. [testng] [2024-11-21 15:34:17,659] [pool-1-thread-10] Initializing /data/dennis/kidney_TFl_Four.bmp: [testng] 15:34:17,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 15:34:17,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:34:17,660 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-21_15-34-17.log] [testng] 15:34:17,660 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5607595c - End of configuration. [testng] [2024-11-21 15:34:17,786] [pool-1-thread-9] Initializing /data/big-images/6kx6k.bmp: [testng] 15:34:17,787 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 15:34:17,787 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:34:17,788 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-21_15-34-17.log] [testng] 15:34:17,788 |-INFO in ch.qos.logback.core.sift.SiftProcessor@720dfd7b - End of configuration. [testng] [2024-11-21 15:34:17,906] [pool-1-thread-8] Initializing /data/dennis/kidney_TFl_Seven.bmp: [testng] 15:34:17,906 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 15:34:17,906 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:34:17,907 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-21_15-34-17.log] [testng] 15:34:17,907 |-INFO in ch.qos.logback.core.sift.SiftProcessor@632d9be2 - End of configuration. [testng] [2024-11-21 15:34:18,028] [pool-1-thread-7] Initializing /data/brian/images/kidney_TFl_1_greyscale.bmp: [testng] 15:34:18,028 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 15:34:18,028 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:34:18,029 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-21_15-34-18.log] [testng] 15:34:18,029 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11de1609 - End of configuration. [testng] [2024-11-21 15:34:18,153] [pool-1-thread-6] Initializing /data/dennis/kidney_TFl_Two.bmp: [testng] 15:34:18,153 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 15:34:18,153 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:34:18,154 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-21_15-34-18.log] [testng] 15:34:18,154 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35f263d8 - End of configuration. [testng] [2024-11-21 15:34:18,285] [pool-1-thread-5] Initializing /data/dennis/kidney_TFl_Eight.bmp: [testng] 15:34:18,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 15:34:18,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:34:18,286 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-21_15-34-18.log] [testng] 15:34:18,286 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55fbbd8a - End of configuration. [testng] [2024-11-21 15:34:18,414] [pool-1-thread-4] Initializing /data/frank/cell_mask_error.bmp: [testng] 15:34:18,414 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 15:34:18,414 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:34:18,415 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-21_15-34-18.log] [testng] 15:34:18,416 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52c96973 - End of configuration. [testng] [2024-11-21 15:34:18,539] [pool-1-thread-3] Initializing /data/curtis/image5.bmp: [testng] 15:34:18,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 15:34:18,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:34:18,541 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-21_15-34-18.log] [testng] 15:34:18,541 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e556296 - End of configuration. [testng] [2024-11-21 15:34:18,827] [pool-1-thread-2] Initializing /data/curtis/image4.bmp: [testng] 15:34:18,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 15:34:18,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:34:18,828 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-21_15-34-18.log] [testng] 15:34:18,828 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29277cd1 - End of configuration. [testng] [2024-11-21 15:34:23,276] [pool-1-thread-2] Initializing /data/dennis/kidney_TFl_Five.bmp: [testng] [2024-11-21 15:34:23,548] [pool-1-thread-1] Initializing /data/bk/ch_00.bmp: [testng] [2024-11-21 15:34:23,801] [pool-1-thread-10] Initializing /data/brian/images/raw_a_rg.tiff: [testng] [2024-11-21 15:34:26,541] [pool-1-thread-3] Initializing /data/curtis/image3.bmp: [testng] [2024-11-21 15:34:26,711] [pool-1-thread-7] Initializing /data/big-images/8kx8k.bmp: [testng] [2024-11-21 15:34:26,869] [pool-1-thread-4] Initializing /data/stephane/holo0908.bmp: [testng] [2024-11-21 15:34:27,032] [pool-1-thread-12] Initializing /data/brian/images/DMSOHigh_001.bmp: [testng] [2024-11-21 15:34:27,225] [pool-1-thread-6] Initializing /data/big-images/8kx8k-grey.bmp: [testng] [2024-11-21 15:34:27,407] [pool-1-thread-8] Initializing /data/brian/images/kidney_TFl_1.bmp: [testng] [2024-11-21 15:34:27,587] [pool-1-thread-5] Initializing /data/dennis/kidney_TFl_Six.bmp: [testng] [2024-11-21 15:34:27,846] [pool-1-thread-11] Initializing /data/brian/images/raw_a.bmp: [testng] [2024-11-21 15:34:30,929] [pool-1-thread-3] Initializing /data/dennis/kidney_TFl_Three.bmp: [testng] [2024-11-21 15:34:31,074] [pool-1-thread-8] Initializing /data/curtis/image1.bmp: [testng] [2024-11-21 15:34:31,206] [pool-1-thread-2] Initializing /data/curtis/image2.bmp: [testng] [2024-11-21 15:34:31,353] [pool-1-thread-12] Initializing /data/brian/images/raw_a_rg.bmp: [testng] [2024-11-21 15:34:31,480] [pool-1-thread-11] Initializing /data/ticket-12971/foo.bmp: [testng] [2024-11-21 15:34:31,591] [pool-1-thread-1] Initializing /data/dennis/kidney_TFl_Nine.bmp: [testng] [2024-11-21 15:34:31,703] [pool-1-thread-4] Initializing /data/bk/100427RBTLPC_FD3__A___5_T_001_ch_00_image_00025_Z_001.bmp: [testng] [2024-11-21 15:34:31,819] [pool-1-thread-5] Initializing /data/big-images/6kx6k-grey.bmp: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1643, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 46 seconds Finished: SUCCESS