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Started by upstream project "BIOFORMATS-test-repo" build number 82 originally caused by: Started by upstream project "Trigger" build number 92 originally caused by: Started by timer 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/jenkins18044000041395830648.sh + '[' bmp = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_12462_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] 01:20:57,369 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:20:57,371 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 01:20:57,371 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:20:57,372 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:20:57,373 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:20:57,373 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:20:57,374 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:20:57,374 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:20:57,374 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:20:57,375 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:20:57,375 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:20:57,376 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:20:57,582 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:20:57,582 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:20:57,610 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:20:57,610 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:20:57,618 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:20:57,618 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:20:57,618 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:20:57,619 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:20:57,619 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 01:20:57,620 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 01:20:57,620 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 246 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-04 01:20:57,633] [main] java.version = 11.0.16 [testng] 01:20:57,637 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:20:57,637 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:57,694 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-04_01-20-57.log] [testng] 01:20:57,695 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-06-04 01:20:57,697] [main] testng.directory = /data [testng] [2024-06-04 01:20:57,698] [main] testng.configDirectory = /config [testng] [2024-06-04 01:20:57,712] [main] testng.multiplier = 1.0 [testng] [2024-06-04 01:20:57,714] [main] testng.in-memory = false [testng] [2024-06-04 01:20:57,714] [main] testng.allow-missing = false [testng] [2024-06-04 01:20:57,714] [main] user.language = en [testng] [2024-06-04 01:20:57,714] [main] user.country = ${user.country} [testng] [2024-06-04 01:20:57,714] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-04 01:20:58,282] [main] ---------------------------------------- [testng] [2024-06-04 01:20:58,282] [main] Total files: 31 [testng] [2024-06-04 01:20:58,282] [main] Scan time: 0.567 s (18 ms/file) [testng] [2024-06-04 01:20:58,282] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 31 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-04 01:20:59,908] [pool-1-thread-1] Initializing /data/curtis/image2.bmp: [testng] 01:20:59,910 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:20:59,910 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:59,912 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-04_01-20-59.log] [testng] 01:20:59,913 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7916a6e5 - End of configuration. [testng] [2024-06-04 01:20:59,930] [pool-1-thread-12] Initializing /data/brian/images/DMSOHigh_001.bmp: [testng] 01:20:59,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:20:59,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:59,932 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-04_01-20-59.log] [testng] 01:20:59,933 |-INFO in ch.qos.logback.core.sift.SiftProcessor@163c3554 - End of configuration. [testng] [2024-06-04 01:20:59,946] [pool-1-thread-11] Initializing /data/bk/ch_00.bmp: [testng] 01:20:59,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:20:59,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:59,947 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-04_01-20-59.log] [testng] 01:20:59,948 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1605c515 - End of configuration. [testng] [2024-06-04 01:20:59,959] [pool-1-thread-10] Initializing /data/ticket-12971/foo.bmp: [testng] 01:20:59,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:20:59,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:59,960 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-04_01-20-59.log] [testng] 01:20:59,960 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d7c47b3 - End of configuration. [testng] [2024-06-04 01:20:59,967] [pool-1-thread-9] Initializing /data/dennis/kidney_TFl_Three.bmp: [testng] 01:20:59,967 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:20:59,967 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:59,968 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-04_01-20-59.log] [testng] 01:20:59,968 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e7629f9 - End of configuration. [testng] [2024-06-04 01:20:59,981] [pool-1-thread-8] Initializing /data/big-images/6kx6k.bmp: [testng] 01:20:59,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:20:59,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:59,982 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-04_01-20-59.log] [testng] 01:20:59,982 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b18878b - End of configuration. [testng] [2024-06-04 01:20:59,994] [pool-1-thread-7] Initializing /data/curtis/image1.bmp: [testng] 01:20:59,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:20:59,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:20:59,995 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-04_01-20-59.log] [testng] 01:20:59,996 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39ccd99b - End of configuration. [testng] [2024-06-04 01:21:00,057] [pool-1-thread-6] Initializing /data/brian/images/kidney_TFl_1.bmp: [testng] 01:21:00,057 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:21:00,057 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:00,058 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-04_01-21-00.log] [testng] 01:21:00,058 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67e36293 - End of configuration. [testng] [2024-06-04 01:21:00,071] [pool-1-thread-5] Initializing /data/dennis/kidney_TFl_Two.bmp: [testng] 01:21:00,071 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:21:00,071 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:00,072 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-04_01-21-00.log] [testng] 01:21:00,073 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3054a5d - End of configuration. [testng] [2024-06-04 01:21:00,094] [pool-1-thread-4] Initializing /data/curtis/image3.bmp: [testng] 01:21:00,095 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:21:00,095 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:00,095 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-04_01-21-00.log] [testng] 01:21:00,096 |-INFO in ch.qos.logback.core.sift.SiftProcessor@233e9178 - End of configuration. [testng] [2024-06-04 01:21:00,109] [pool-1-thread-3] Initializing /data/brian/images/raw_a_rg.tiff: [testng] 01:21:00,109 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:21:00,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:00,111 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-04_01-21-00.log] [testng] 01:21:00,111 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28488088 - End of configuration. [testng] [2024-06-04 01:21:00,157] [pool-1-thread-2] Initializing /data/dennis/kidney_TFl_Four.bmp: [testng] 01:21:00,157 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:21:00,158 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:21:00,158 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-04_01-21-00.log] [testng] 01:21:00,159 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d8ec232 - End of configuration. [testng] [2024-06-04 01:21:03,003] [pool-1-thread-5] Initializing /data/dennis/kidney_TFl_Seven.bmp: [testng] [2024-06-04 01:21:03,011] [pool-1-thread-4] Initializing /data/dennis/kidney_TFl_Nine.bmp: [testng] [2024-06-04 01:21:03,018] [pool-1-thread-12] Initializing /data/big-images/8kx8k-grey.bmp: [testng] [2024-06-04 01:21:03,026] [pool-1-thread-3] Initializing /data/brian/images/raw_a_rg.bmp: [testng] [2024-06-04 01:21:03,030] [pool-1-thread-11] Initializing /data/dennis/kidney_TFl_One.bmp: [testng] [2024-06-04 01:21:03,035] [pool-1-thread-2] Initializing /data/curtis/image5.bmp: [testng] [2024-06-04 01:21:03,039] [pool-1-thread-6] Initializing /data/dennis/kidney_TFl_Five.bmp: [testng] [2024-06-04 01:21:03,070] [pool-1-thread-9] Initializing /data/qa-4538/22577136_Figure 2_A_ATF6 (GST)_13572.bmp: [testng] [2024-06-04 01:21:03,079] [pool-1-thread-10] Initializing /data/dennis/kidney_TFl_Six.bmp: [testng] [2024-06-04 01:21:03,088] [pool-1-thread-7] Initializing /data/stephane/holo0908.bmp: [testng] [2024-06-04 01:21:03,096] [pool-1-thread-1] Initializing /data/frank/cell_mask_error.bmp: [testng] [2024-06-04 01:21:03,866] [pool-1-thread-2] Initializing /data/bk/100427RBTLPC_FD3__A___5_T_001_ch_00_image_00025_Z_001.bmp: [testng] [2024-06-04 01:21:04,014] [pool-1-thread-3] Initializing /data/brian/images/kidney_TFl_1_greyscale.bmp: [testng] [2024-06-04 01:21:04,147] [pool-1-thread-4] Initializing /data/curtis/image4.bmp: [testng] [2024-06-04 01:21:04,151] [pool-1-thread-10] Initializing /data/brian/images/raw_a.bmp: [testng] [2024-06-04 01:21:04,155] [pool-1-thread-11] Initializing /data/big-images/8kx8k.bmp: [testng] [2024-06-04 01:21:04,195] [pool-1-thread-1] Initializing /data/big-images/6kx6k-grey.bmp: [testng] [2024-06-04 01:21:04,202] [pool-1-thread-6] Initializing /data/brian/images/23srp5dksub.bmp: [testng] [2024-06-04 01:21:04,225] [pool-1-thread-5] 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: 38 seconds Finished: SUCCESS