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Started by upstream project "BIOFORMATS-test-repo" build number 293 originally caused by: Started by upstream project "Trigger" build number 312 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins13702909403858595810.sh + '[' bmp = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_46267_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] 00:37:47,346 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:37:47,347 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 00:37:47,347 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:37:47,348 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:37:47,349 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:37:47,349 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:37:47,350 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:37:47,350 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:37:47,350 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:37:47,351 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:37:47,351 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:37:47,351 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:37:47,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:37:47,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:37:47,550 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:37:47,550 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:37:47,556 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:37:47,556 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:37:47,556 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:37:47,556 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:37:47,557 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 00:37:47,557 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 00:37:47,557 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 207 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-17 00:37:47,567] [main] java.version = 11.0.16 [testng] 00:37:47,570 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:37:47,570 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:47,613 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-17_00-37-47.log] [testng] 00:37:47,615 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-12-17 00:37:47,617] [main] testng.directory = /data [testng] [2024-12-17 00:37:47,617] [main] testng.configDirectory = /config [testng] [2024-12-17 00:37:47,627] [main] testng.multiplier = 1.0 [testng] [2024-12-17 00:37:47,628] [main] testng.in-memory = false [testng] [2024-12-17 00:37:47,628] [main] testng.allow-missing = false [testng] [2024-12-17 00:37:47,628] [main] user.language = en [testng] [2024-12-17 00:37:47,628] [main] user.country = ${user.country} [testng] [2024-12-17 00:37:47,628] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-17 00:37:49,215] [main] ---------------------------------------- [testng] [2024-12-17 00:37:49,216] [main] Total files: 31 [testng] [2024-12-17 00:37:49,216] [main] Scan time: 1.586 s (51 ms/file) [testng] [2024-12-17 00:37:49,216] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 31 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-17 00:38:04,128] [pool-1-thread-1] Initializing /data/bk/100427RBTLPC_FD3__A___5_T_001_ch_00_image_00025_Z_001.bmp: [testng] 00:38:04,130 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:38:04,130 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:04,133 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-17_00-38-04.log] [testng] 00:38:04,134 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a5538e6 - End of configuration. [testng] [2024-12-17 00:38:04,442] [pool-1-thread-12] Initializing /data/brian/images/DMSOHigh_001.bmp: [testng] 00:38:04,442 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:38:04,442 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:04,443 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-17_00-38-04.log] [testng] 00:38:04,444 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10c27f66 - End of configuration. [testng] [2024-12-17 00:38:04,765] [pool-1-thread-11] Initializing /data/dennis/kidney_TFl_Seven.bmp: [testng] 00:38:04,765 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:38:04,766 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:04,766 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-17_00-38-04.log] [testng] 00:38:04,766 |-INFO in ch.qos.logback.core.sift.SiftProcessor@266e64f7 - End of configuration. [testng] [2024-12-17 00:38:06,240] [pool-1-thread-10] Initializing /data/curtis/image4.bmp: [testng] 00:38:06,240 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:38:06,241 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:06,241 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-17_00-38-06.log] [testng] 00:38:06,241 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e7498d - End of configuration. [testng] [2024-12-17 00:38:07,097] [pool-1-thread-9] Initializing /data/dennis/kidney_TFl_Six.bmp: [testng] 00:38:07,097 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:38:07,097 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:07,098 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-17_00-38-07.log] [testng] 00:38:07,098 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e309c0f - End of configuration. [testng] [2024-12-17 00:38:07,252] [pool-1-thread-8] Initializing /data/dennis/kidney_TFl_Eight.bmp: [testng] 00:38:07,253 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:38:07,253 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:07,253 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-17_00-38-07.log] [testng] 00:38:07,254 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7772c0c7 - End of configuration. [testng] [2024-12-17 00:38:07,407] [pool-1-thread-7] Initializing /data/curtis/image2.bmp: [testng] 00:38:07,407 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:38:07,407 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:07,407 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-17_00-38-07.log] [testng] 00:38:07,408 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27dd0921 - End of configuration. [testng] [2024-12-17 00:38:07,560] [pool-1-thread-6] Initializing /data/stephane/holo0908.bmp: [testng] 00:38:07,560 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:38:07,560 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:07,561 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-17_00-38-07.log] [testng] 00:38:07,561 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d582384 - End of configuration. [testng] [2024-12-17 00:38:07,974] [pool-1-thread-5] Initializing /data/brian/images/kidney_TFl_1_greyscale.bmp: [testng] 00:38:07,974 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:38:07,974 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:07,975 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-17_00-38-07.log] [testng] 00:38:07,975 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58c7f41b - End of configuration. [testng] [2024-12-17 00:38:08,293] [pool-1-thread-4] Initializing /data/qa-4538/22577136_Figure 2_A_ATF6 (GST)_13572.bmp: [testng] 00:38:08,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:38:08,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:08,294 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-17_00-38-08.log] [testng] 00:38:08,294 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46bbdd71 - End of configuration. [testng] [2024-12-17 00:38:08,504] [pool-1-thread-3] Initializing /data/dennis/kidney_TFl_Three.bmp: [testng] 00:38:08,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:38:08,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:08,505 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-17_00-38-08.log] [testng] 00:38:08,506 |-INFO in ch.qos.logback.core.sift.SiftProcessor@96a38ef - End of configuration. [testng] [2024-12-17 00:38:08,731] [pool-1-thread-2] Initializing /data/brian/images/raw_a.bmp: [testng] 00:38:08,731 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:38:08,731 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:08,732 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-17_00-38-08.log] [testng] 00:38:08,732 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a3f3cf1 - End of configuration. [testng] [2024-12-17 00:38:13,989] [pool-1-thread-9] Initializing /data/frank/cell_mask_error.bmp: [testng] [2024-12-17 00:38:14,141] [pool-1-thread-11] Initializing /data/dennis/kidney_TFl_Nine.bmp: [testng] [2024-12-17 00:38:14,286] [pool-1-thread-5] Initializing /data/bk/ch_00.bmp: [testng] [2024-12-17 00:38:14,433] [pool-1-thread-8] Initializing /data/brian/images/23srp5dksub.bmp: [testng] [2024-12-17 00:38:14,583] [pool-1-thread-3] Initializing /data/big-images/6kx6k.bmp: [testng] [2024-12-17 00:38:14,761] [pool-1-thread-2] Initializing /data/big-images/8kx8k.bmp: [testng] [2024-12-17 00:38:14,913] [pool-1-thread-10] Initializing /data/brian/images/raw_a_rg.tiff: [testng] [2024-12-17 00:38:16,914] [pool-1-thread-7] Initializing /data/brian/images/kidney_TFl_1.bmp: [testng] [2024-12-17 00:38:17,083] [pool-1-thread-12] Initializing /data/dennis/kidney_TFl_Four.bmp: [testng] [2024-12-17 00:38:17,237] [pool-1-thread-6] Initializing /data/curtis/image5.bmp: [testng] [2024-12-17 00:38:17,376] [pool-1-thread-1] Initializing /data/curtis/image1.bmp: [testng] [2024-12-17 00:38:17,520] [pool-1-thread-4] Initializing /data/brian/images/raw_a_rg.bmp: [testng] [2024-12-17 00:38:20,401] [pool-1-thread-6] Initializing /data/dennis/kidney_TFl_One.bmp: [testng] [2024-12-17 00:38:20,609] [pool-1-thread-1] Initializing /data/big-images/6kx6k-grey.bmp: [testng] [2024-12-17 00:38:20,778] [pool-1-thread-9] Initializing /data/big-images/8kx8k-grey.bmp: [testng] [2024-12-17 00:38:20,967] [pool-1-thread-7] Initializing /data/dennis/kidney_TFl_Two.bmp: [testng] [2024-12-17 00:38:21,167] [pool-1-thread-4] Initializing /data/ticket-12971/foo.bmp: [testng] [2024-12-17 00:38:21,366] [pool-1-thread-11] Initializing /data/dennis/kidney_TFl_Five.bmp: [testng] [2024-12-17 00:38:21,628] [pool-1-thread-12] 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: 59 seconds Finished: SUCCESS