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Started by upstream project "BIOFORMATS-test-repo" build number 361 originally caused by: Started by upstream project "Trigger" build number 387 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins6498183481443157378.sh + '[' bmp = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_57493_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] 00:27:22,909 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:27:22,910 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - No custom configurators were discovered as a service. [testng] 00:27:22,910 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:27:22,911 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:27:22,912 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:27:22,912 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:27:22,912 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:27:22,912 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:27:22,913 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:27:22,914 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:27:22,914 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:27:22,914 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:27:23,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:27:23,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:27:23,115 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:27:23,115 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:27:23,120 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:27:23,121 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:27:23,121 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:27:23,121 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:27:23,121 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@65c7a252 - End of configuration. [testng] 00:27:23,122 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@38cee291 - Registering current configuration as safe fallback point [testng] 00:27:23,122 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 209 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-01 00:27:23,131] [main] java.version = 11.0.16 [testng] 00:27:23,134 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:27:23,134 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:23,177 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-01_00-27-23.log] [testng] 00:27:23,178 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13d73f29 - End of configuration. [testng] [2025-03-01 00:27:23,180] [main] testng.directory = /data [testng] [2025-03-01 00:27:23,180] [main] testng.configDirectory = /config [testng] [2025-03-01 00:27:23,191] [main] testng.multiplier = 1.0 [testng] [2025-03-01 00:27:23,192] [main] testng.in-memory = false [testng] [2025-03-01 00:27:23,192] [main] testng.allow-missing = false [testng] [2025-03-01 00:27:23,192] [main] user.language = en [testng] [2025-03-01 00:27:23,192] [main] user.country = ${user.country} [testng] [2025-03-01 00:27:23,193] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-01 00:27:24,006] [main] ---------------------------------------- [testng] [2025-03-01 00:27:24,006] [main] Total files: 31 [testng] [2025-03-01 00:27:24,006] [main] Scan time: 0.812 s (26 ms/file) [testng] [2025-03-01 00:27:24,006] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 31 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-01 00:27:28,575] [pool-1-thread-1] Initializing /data/brian/images/raw_a_rg.bmp: [testng] 00:27:28,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:27:28,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:28,578 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-01_00-27-28.log] [testng] 00:27:28,578 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ae52cab - End of configuration. [testng] [2025-03-01 00:27:28,714] [pool-1-thread-12] Initializing /data/stephane/holo0908.bmp: [testng] 00:27:28,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:27:28,715 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:28,715 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-01_00-27-28.log] [testng] 00:27:28,716 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31bf532 - End of configuration. [testng] [2025-03-01 00:27:28,836] [pool-1-thread-11] Initializing /data/bk/100427RBTLPC_FD3__A___5_T_001_ch_00_image_00025_Z_001.bmp: [testng] 00:27:28,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:27:28,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:28,837 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-01_00-27-28.log] [testng] 00:27:28,837 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71cc116e - End of configuration. [testng] [2025-03-01 00:27:28,963] [pool-1-thread-10] Initializing /data/big-images/8kx8k-grey.bmp: [testng] 00:27:28,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:27:28,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:28,964 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-01_00-27-28.log] [testng] 00:27:28,965 |-INFO in ch.qos.logback.core.sift.SiftProcessor@425ef382 - End of configuration. [testng] [2025-03-01 00:27:29,155] [pool-1-thread-9] Initializing /data/frank/cell_mask_error.bmp: [testng] 00:27:29,155 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:27:29,155 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:29,156 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-01_00-27-29.log] [testng] 00:27:29,156 |-INFO in ch.qos.logback.core.sift.SiftProcessor@edb393b - End of configuration. [testng] [2025-03-01 00:27:29,291] [pool-1-thread-8] Initializing /data/dennis/kidney_TFl_One.bmp: [testng] 00:27:29,291 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:27:29,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:29,292 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-01_00-27-29.log] [testng] 00:27:29,293 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1989ef7c - End of configuration. [testng] [2025-03-01 00:27:29,428] [pool-1-thread-7] Initializing /data/brian/images/raw_a.bmp: [testng] 00:27:29,429 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:27:29,429 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:29,430 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-01_00-27-29.log] [testng] 00:27:29,430 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31d7adfb - End of configuration. [testng] [2025-03-01 00:27:29,720] [pool-1-thread-6] Initializing /data/bk/ch_00.bmp: [testng] 00:27:29,721 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:27:29,721 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:29,721 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-01_00-27-29.log] [testng] 00:27:29,721 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18d95773 - End of configuration. [testng] [2025-03-01 00:27:30,241] [pool-1-thread-5] Initializing /data/dennis/kidney_TFl_Seven.bmp: [testng] 00:27:30,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:27:30,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:30,242 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-01_00-27-30.log] [testng] 00:27:30,242 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bac7cd7 - End of configuration. [testng] [2025-03-01 00:27:30,359] [pool-1-thread-4] Initializing /data/brian/images/raw_a_rg.tiff: [testng] 00:27:30,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:27:30,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:30,360 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-01_00-27-30.log] [testng] 00:27:30,361 |-INFO in ch.qos.logback.core.sift.SiftProcessor@585d15fa - End of configuration. [testng] [2025-03-01 00:27:32,235] [pool-1-thread-3] Initializing /data/brian/images/kidney_TFl_1_greyscale.bmp: [testng] 00:27:32,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:27:32,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:32,236 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-01_00-27-32.log] [testng] 00:27:32,237 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e5b4840 - End of configuration. [testng] [2025-03-01 00:27:32,356] [pool-1-thread-2] Initializing /data/curtis/image5.bmp: [testng] 00:27:32,357 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:27:32,357 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:32,357 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-01_00-27-32.log] [testng] 00:27:32,358 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d9bb08 - End of configuration. [testng] [2025-03-01 00:27:34,975] [pool-1-thread-2] Initializing /data/dennis/kidney_TFl_Four.bmp: [testng] [2025-03-01 00:27:35,041] [pool-1-thread-1] Initializing /data/curtis/image4.bmp: [testng] [2025-03-01 00:27:35,107] [pool-1-thread-7] Initializing /data/dennis/kidney_TFl_Three.bmp: [testng] [2025-03-01 00:27:35,176] [pool-1-thread-3] Initializing /data/dennis/kidney_TFl_Nine.bmp: [testng] [2025-03-01 00:27:35,244] [pool-1-thread-5] Initializing /data/ticket-12971/foo.bmp: [testng] [2025-03-01 00:27:35,304] [pool-1-thread-8] Initializing /data/dennis/kidney_TFl_Two.bmp: [testng] [2025-03-01 00:27:35,366] [pool-1-thread-9] Initializing /data/dennis/kidney_TFl_Six.bmp: [testng] [2025-03-01 00:27:35,490] [pool-1-thread-12] Initializing /data/curtis/image2.bmp: [testng] [2025-03-01 00:27:35,585] [pool-1-thread-11] Initializing /data/dennis/kidney_TFl_Five.bmp: [testng] [2025-03-01 00:27:35,792] [pool-1-thread-6] Initializing /data/brian/images/kidney_TFl_1.bmp: [testng] [2025-03-01 00:27:36,670] [pool-1-thread-1] Initializing /data/dennis/kidney_TFl_Eight.bmp: [testng] [2025-03-01 00:27:36,746] [pool-1-thread-5] Initializing /data/big-images/6kx6k.bmp: [testng] [2025-03-01 00:27:36,836] [pool-1-thread-7] Initializing /data/qa-4538/22577136_Figure 2_A_ATF6 (GST)_13572.bmp: [testng] [2025-03-01 00:27:36,914] [pool-1-thread-9] Initializing /data/big-images/6kx6k-grey.bmp: [testng] [2025-03-01 00:27:36,978] [pool-1-thread-3] Initializing /data/curtis/image1.bmp: [testng] [2025-03-01 00:27:37,076] [pool-1-thread-8] Initializing /data/brian/images/23srp5dksub.bmp: [testng] [2025-03-01 00:27:37,187] [pool-1-thread-2] Initializing /data/brian/images/DMSOHigh_001.bmp: [testng] [2025-03-01 00:27:37,311] [pool-1-thread-12] Initializing /data/big-images/8kx8k.bmp: [testng] [2025-03-01 00:27:37,821] [pool-1-thread-11] Initializing /data/curtis/image3.bmp: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1643, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 42 seconds Finished: SUCCESS