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Started by upstream project "BIOFORMATS-test-repo" build number 225 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins13195038052693634046.sh + '[' bmp = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35456_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 11:21:05,190 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 11:21:05,191 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 11:21:05,191 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:21:05,192 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:21:05,193 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 11:21:05,193 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 11:21:05,193 |-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] 11:21:05,193 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:21:05,194 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:21:05,194 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 11:21:05,195 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:21:05,195 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:21:05,350 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:21:05,350 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:21:05,386 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:21:05,386 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:21:05,392 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:21:05,392 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:21:05,393 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:21:05,393 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:21:05,393 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 11:21:05,394 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 11:21:05,394 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 200 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-17 11:21:05,403] [main] java.version = 21 [testng] 11:21:05,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:21:05,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:21:05,445 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-17_11-21-05.log] [testng] 11:21:05,446 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-10-17 11:21:05,448] [main] testng.directory = /data [testng] [2024-10-17 11:21:05,448] [main] testng.configDirectory = /config [testng] [2024-10-17 11:21:05,456] [main] testng.multiplier = 1.0 [testng] [2024-10-17 11:21:05,457] [main] testng.in-memory = false [testng] [2024-10-17 11:21:05,457] [main] testng.allow-missing = false [testng] [2024-10-17 11:21:05,457] [main] user.language = en [testng] [2024-10-17 11:21:05,457] [main] user.country = ${user.country} [testng] [2024-10-17 11:21:05,457] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-17 11:21:06,657] [main] ---------------------------------------- [testng] [2024-10-17 11:21:06,657] [main] Total files: 31 [testng] [2024-10-17 11:21:06,657] [main] Scan time: 1.2 s (38 ms/file) [testng] [2024-10-17 11:21:06,658] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 31 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-17 11:21:28,448] [pool-1-thread-1] Initializing /data/dennis/kidney_TFl_One.bmp: [testng] 11:21:28,450 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 11:21:28,450 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:21:28,452 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-17_11-21-28.log] [testng] 11:21:28,453 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61925d76 - End of configuration. [testng] [2024-10-17 11:21:28,818] [pool-1-thread-12] Initializing /data/brian/images/23srp5dksub.bmp: [testng] 11:21:28,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 11:21:28,818 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:21:28,819 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-17_11-21-28.log] [testng] 11:21:28,819 |-INFO in ch.qos.logback.core.sift.SiftProcessor@632d9be2 - End of configuration. [testng] [2024-10-17 11:21:29,262] [pool-1-thread-11] Initializing /data/qa-4538/22577136_Figure 2_A_ATF6 (GST)_13572.bmp: [testng] 11:21:29,262 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 11:21:29,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:21:29,263 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-17_11-21-29.log] [testng] 11:21:29,264 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11de1609 - End of configuration. [testng] [2024-10-17 11:21:29,492] [pool-1-thread-10] Initializing /data/dennis/kidney_TFl_Four.bmp: [testng] 11:21:29,493 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 11:21:29,493 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:21:29,494 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-17_11-21-29.log] [testng] 11:21:29,494 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35f263d8 - End of configuration. [testng] [2024-10-17 11:21:30,172] [pool-1-thread-9] Initializing /data/big-images/6kx6k.bmp: [testng] 11:21:30,172 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 11:21:30,172 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:21:30,173 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-17_11-21-30.log] [testng] 11:21:30,173 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55fbbd8a - End of configuration. [testng] [2024-10-17 11:21:31,224] [pool-1-thread-8] Initializing /data/dennis/kidney_TFl_Seven.bmp: [testng] 11:21:31,225 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 11:21:31,225 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:21:31,225 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-17_11-21-31.log] [testng] 11:21:31,226 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52c96973 - End of configuration. [testng] [2024-10-17 11:21:32,203] [pool-1-thread-7] Initializing /data/brian/images/kidney_TFl_1_greyscale.bmp: [testng] 11:21:32,203 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 11:21:32,203 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:21:32,204 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-17_11-21-32.log] [testng] 11:21:32,204 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e556296 - End of configuration. [testng] [2024-10-17 11:21:33,100] [pool-1-thread-6] Initializing /data/dennis/kidney_TFl_Two.bmp: [testng] 11:21:33,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 11:21:33,100 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:21:33,101 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-17_11-21-33.log] [testng] 11:21:33,101 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29277cd1 - End of configuration. [testng] [2024-10-17 11:21:34,322] [pool-1-thread-5] Initializing /data/dennis/kidney_TFl_Eight.bmp: [testng] 11:21:34,322 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 11:21:34,322 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:21:34,323 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-17_11-21-34.log] [testng] 11:21:34,324 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e59efbc - End of configuration. [testng] [2024-10-17 11:21:35,048] [pool-1-thread-4] Initializing /data/frank/cell_mask_error.bmp: [testng] 11:21:35,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 11:21:35,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:21:35,049 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-17_11-21-35.log] [testng] 11:21:35,050 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e25aff7 - End of configuration. [testng] [2024-10-17 11:21:35,383] [pool-1-thread-3] Initializing /data/curtis/image5.bmp: [testng] 11:21:35,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 11:21:35,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:21:35,384 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-17_11-21-35.log] [testng] 11:21:35,385 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b4db33a - End of configuration. [testng] [2024-10-17 11:21:35,764] [pool-1-thread-2] Initializing /data/curtis/image4.bmp: [testng] 11:21:35,765 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 11:21:35,765 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:21:35,765 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-17_11-21-35.log] [testng] 11:21:35,766 |-INFO in ch.qos.logback.core.sift.SiftProcessor@567e122b - End of configuration. [testng] [2024-10-17 11:21:46,999] [pool-1-thread-2] Initializing /data/dennis/kidney_TFl_Five.bmp: [testng] [2024-10-17 11:21:47,859] [pool-1-thread-11] Initializing /data/brian/images/raw_a.bmp: [testng] [2024-10-17 11:21:48,321] [pool-1-thread-3] Initializing /data/big-images/8kx8k-grey.bmp: [testng] [2024-10-17 11:21:48,625] [pool-1-thread-7] Initializing /data/brian/images/kidney_TFl_1.bmp: [testng] [2024-10-17 11:21:49,078] [pool-1-thread-1] Initializing /data/dennis/kidney_TFl_Six.bmp: [testng] [2024-10-17 11:21:50,027] [pool-1-thread-8] Initializing /data/brian/images/DMSOHigh_001.bmp: [testng] [2024-10-17 11:21:50,777] [pool-1-thread-5] Initializing /data/bk/ch_00.bmp: [testng] [2024-10-17 11:21:51,399] [pool-1-thread-10] Initializing /data/brian/images/raw_a_rg.tiff: [testng] [2024-10-17 11:21:56,203] [pool-1-thread-4] Initializing /data/curtis/image3.bmp: [testng] [2024-10-17 11:21:56,502] [pool-1-thread-6] Initializing /data/big-images/8kx8k.bmp: [testng] [2024-10-17 11:21:56,617] [pool-1-thread-12] Initializing /data/stephane/holo0908.bmp: [testng] [2024-10-17 11:21:59,137] [pool-1-thread-9] Initializing /data/dennis/kidney_TFl_Three.bmp: [testng] [2024-10-17 11:22:02,626] [pool-1-thread-4] Initializing /data/curtis/image2.bmp: [testng] [2024-10-17 11:22:03,140] [pool-1-thread-11] Initializing /data/curtis/image1.bmp: [testng] [2024-10-17 11:22:03,630] [pool-1-thread-1] Initializing /data/dennis/kidney_TFl_Nine.bmp: [testng] [2024-10-17 11:22:04,030] [pool-1-thread-2] Initializing /data/bk/100427RBTLPC_FD3__A___5_T_001_ch_00_image_00025_Z_001.bmp: [testng] [2024-10-17 11:22:04,095] [pool-1-thread-5] Initializing /data/big-images/6kx6k-grey.bmp: [testng] [2024-10-17 11:22:04,172] [pool-1-thread-8] Initializing /data/brian/images/raw_a_rg.bmp: [testng] [2024-10-17 11:22:04,252] [pool-1-thread-12] 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: 1 minute 19 seconds Finished: SUCCESS