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Started by upstream project "BIOFORMATS-test-repo" build number 312 originally caused by: Started by upstream project "Trigger" build number 334 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/jenkins6586660986754125181.sh + '[' bmp = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_49403_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] 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] 00:29:19,950 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:29:19,951 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:29:19,951 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:29:19,952 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:29:19,953 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:29:19,953 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:29:19,953 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:29:19,953 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:29:19,954 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:29:19,955 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:29:19,955 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:29:19,955 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:29:20,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:29:20,122 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:29:20,144 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:29:20,144 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:29:20,149 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:29:20,149 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:29:20,149 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:29:20,150 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:29:20,150 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:29:20,151 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:29:20,151 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 197 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-01-08 00:29:20,160] [main] java.version = 17.0.2 [testng] 00:29:20,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:29:20,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:20,204 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-08_00-29-20.log] [testng] 00:29:20,205 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2025-01-08 00:29:20,207] [main] testng.directory = /data [testng] [2025-01-08 00:29:20,208] [main] testng.configDirectory = /config [testng] [2025-01-08 00:29:20,216] [main] testng.multiplier = 1.0 [testng] [2025-01-08 00:29:20,217] [main] testng.in-memory = false [testng] [2025-01-08 00:29:20,217] [main] testng.allow-missing = false [testng] [2025-01-08 00:29:20,217] [main] user.language = en [testng] [2025-01-08 00:29:20,217] [main] user.country = ${user.country} [testng] [2025-01-08 00:29:20,217] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-01-08 00:29:21,286] [main] ---------------------------------------- [testng] [2025-01-08 00:29:21,286] [main] Total files: 31 [testng] [2025-01-08 00:29:21,286] [main] Scan time: 1.069 s (34 ms/file) [testng] [2025-01-08 00:29:21,286] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 31 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-08 00:29:26,194] [pool-1-thread-1] Initializing /data/dennis/kidney_TFl_Five.bmp: [testng] 00:29:26,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:29:26,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:26,196 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-08_00-29-26.log] [testng] 00:29:26,196 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4df2f7f5 - End of configuration. [testng] [2025-01-08 00:29:26,269] [pool-1-thread-12] Initializing /data/stephane/holo0908.bmp: [testng] 00:29:26,269 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:29:26,269 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:26,270 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-08_00-29-26.log] [testng] 00:29:26,270 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7760d922 - End of configuration. [testng] [2025-01-08 00:29:26,342] [pool-1-thread-11] Initializing /data/curtis/image2.bmp: [testng] 00:29:26,343 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:29:26,343 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:26,344 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-08_00-29-26.log] [testng] 00:29:26,344 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10afdf7 - End of configuration. [testng] [2025-01-08 00:29:26,413] [pool-1-thread-10] Initializing /data/dennis/kidney_TFl_Two.bmp: [testng] 00:29:26,413 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:29:26,414 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:26,414 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-08_00-29-26.log] [testng] 00:29:26,415 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77294ace - End of configuration. [testng] [2025-01-08 00:29:26,498] [pool-1-thread-9] Initializing /data/dennis/kidney_TFl_Eight.bmp: [testng] 00:29:26,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:29:26,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:26,499 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-08_00-29-26.log] [testng] 00:29:26,499 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ea0c1f0 - End of configuration. [testng] [2025-01-08 00:29:26,557] [pool-1-thread-8] Initializing /data/brian/images/kidney_TFl_1_greyscale.bmp: [testng] 00:29:26,557 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:29:26,557 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:26,558 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-08_00-29-26.log] [testng] 00:29:26,558 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2aead771 - End of configuration. [testng] [2025-01-08 00:29:26,614] [pool-1-thread-7] Initializing /data/curtis/image5.bmp: [testng] 00:29:26,614 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:29:26,614 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:26,615 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-08_00-29-26.log] [testng] 00:29:26,615 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63433986 - End of configuration. [testng] [2025-01-08 00:29:26,675] [pool-1-thread-6] Initializing /data/brian/images/raw_a_rg.tiff: [testng] 00:29:26,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:29:26,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:26,676 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-08_00-29-26.log] [testng] 00:29:26,676 |-INFO in ch.qos.logback.core.sift.SiftProcessor@425061d1 - End of configuration. [testng] [2025-01-08 00:29:27,478] [pool-1-thread-5] Initializing /data/brian/images/raw_a.bmp: [testng] 00:29:27,478 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:29:27,478 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:27,479 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-08_00-29-27.log] [testng] 00:29:27,479 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6334d8f - End of configuration. [testng] [2025-01-08 00:29:27,552] [pool-1-thread-4] Initializing /data/frank/cell_mask_error.bmp: [testng] 00:29:27,553 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:29:27,553 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:27,554 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-08_00-29-27.log] [testng] 00:29:27,555 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ee2c984 - End of configuration. [testng] [2025-01-08 00:29:27,614] [pool-1-thread-3] Initializing /data/brian/images/DMSOHigh_001.bmp: [testng] 00:29:27,614 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:29:27,614 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:27,615 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-08_00-29-27.log] [testng] 00:29:27,615 |-INFO in ch.qos.logback.core.sift.SiftProcessor@649845c5 - End of configuration. [testng] [2025-01-08 00:29:27,678] [pool-1-thread-2] Initializing /data/bk/100427RBTLPC_FD3__A___5_T_001_ch_00_image_00025_Z_001.bmp: [testng] 00:29:27,679 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:29:27,679 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:29:27,680 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-08_00-29-27.log] [testng] 00:29:27,681 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b7d39fa - End of configuration. [testng] [2025-01-08 00:29:30,413] [pool-1-thread-5] Initializing /data/curtis/image1.bmp: [testng] [2025-01-08 00:29:30,483] [pool-1-thread-9] Initializing /data/dennis/kidney_TFl_Three.bmp: [testng] [2025-01-08 00:29:30,555] [pool-1-thread-10] Initializing /data/curtis/image3.bmp: [testng] [2025-01-08 00:29:30,625] [pool-1-thread-11] Initializing /data/dennis/kidney_TFl_One.bmp: [testng] [2025-01-08 00:29:30,696] [pool-1-thread-8] Initializing /data/dennis/kidney_TFl_Seven.bmp: [testng] [2025-01-08 00:29:30,761] [pool-1-thread-7] Initializing /data/dennis/kidney_TFl_Nine.bmp: [testng] [2025-01-08 00:29:30,919] [pool-1-thread-1] Initializing /data/curtis/image4.bmp: [testng] [2025-01-08 00:29:30,988] [pool-1-thread-3] Initializing /data/brian/images/raw_a_rg.bmp: [testng] [2025-01-08 00:29:31,055] [pool-1-thread-4] Initializing /data/big-images/8kx8k-grey.bmp: [testng] [2025-01-08 00:29:31,247] [pool-1-thread-12] Initializing /data/big-images/6kx6k-grey.bmp: [testng] [2025-01-08 00:29:31,643] [pool-1-thread-2] Initializing /data/big-images/8kx8k.bmp: [testng] [2025-01-08 00:29:32,947] [pool-1-thread-5] Initializing /data/dennis/kidney_TFl_Four.bmp: [testng] [2025-01-08 00:29:33,094] [pool-1-thread-10] Initializing /data/ticket-12971/foo.bmp: [testng] [2025-01-08 00:29:33,187] [pool-1-thread-9] Initializing /data/brian/images/23srp5dksub.bmp: [testng] [2025-01-08 00:29:33,286] [pool-1-thread-3] Initializing /data/bk/ch_00.bmp: [testng] [2025-01-08 00:29:33,379] [pool-1-thread-1] Initializing /data/big-images/6kx6k.bmp: [testng] [2025-01-08 00:29:33,468] [pool-1-thread-7] Initializing /data/qa-4538/22577136_Figure 2_A_ATF6 (GST)_13572.bmp: [testng] [2025-01-08 00:29:33,571] [pool-1-thread-8] Initializing /data/dennis/kidney_TFl_Six.bmp: [testng] [2025-01-08 00:29:33,777] [pool-1-thread-11] Initializing /data/brian/images/kidney_TFl_1.bmp: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1643, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 40 seconds Finished: SUCCESS