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Started by upstream project "BIOFORMATS-test-repo" build number 116 originally caused by: Started by upstream project "Trigger" build number 133 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/jenkins16944508226434656836.sh + '[' bmp = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_18038_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] 01:22:51,412 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:22:51,413 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:22:51,413 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:22:51,414 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:22:51,414 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:22:51,415 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:22:51,415 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:22:51,415 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:22:51,415 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:22:51,416 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:22:51,416 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:22:51,417 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:22:51,589 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:22:51,589 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:22:51,616 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:22:51,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:22:51,622 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:22:51,623 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:22:51,623 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:22:51,623 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:22:51,624 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:22:51,625 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:22:51,625 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 210 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-10 01:22:51,634] [main] java.version = 17.0.2 [testng] 01:22:51,638 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:22:51,638 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:51,679 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-10_01-22-51.log] [testng] 01:22:51,681 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-07-10 01:22:51,683] [main] testng.directory = /data [testng] [2024-07-10 01:22:51,683] [main] testng.configDirectory = /config [testng] [2024-07-10 01:22:51,693] [main] testng.multiplier = 1.0 [testng] [2024-07-10 01:22:51,693] [main] testng.in-memory = false [testng] [2024-07-10 01:22:51,694] [main] testng.allow-missing = false [testng] [2024-07-10 01:22:51,694] [main] user.language = en [testng] [2024-07-10 01:22:51,694] [main] user.country = ${user.country} [testng] [2024-07-10 01:22:51,694] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-10 01:22:52,179] [main] ---------------------------------------- [testng] [2024-07-10 01:22:52,179] [main] Total files: 31 [testng] [2024-07-10 01:22:52,180] [main] Scan time: 0.485 s (15 ms/file) [testng] [2024-07-10 01:22:52,180] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 31 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-10 01:22:53,578] [pool-1-thread-1] Initializing /data/bk/ch_00.bmp: [testng] 01:22:53,579 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:22:53,579 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:53,580 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-10_01-22-53.log] [testng] 01:22:53,581 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fb0c1b2 - End of configuration. [testng] [2024-07-10 01:22:53,597] [pool-1-thread-12] Initializing /data/big-images/6kx6k.bmp: [testng] 01:22:53,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:22:53,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:53,598 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-10_01-22-53.log] [testng] 01:22:53,599 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b797bee - End of configuration. [testng] [2024-07-10 01:22:53,625] [pool-1-thread-11] Initializing /data/ticket-12971/foo.bmp: [testng] 01:22:53,625 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:22:53,625 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:53,627 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-10_01-22-53.log] [testng] 01:22:53,627 |-INFO in ch.qos.logback.core.sift.SiftProcessor@376902e6 - End of configuration. [testng] [2024-07-10 01:22:53,637] [pool-1-thread-10] Initializing /data/dennis/kidney_TFl_Three.bmp: [testng] 01:22:53,637 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:22:53,637 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:53,638 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-10_01-22-53.log] [testng] 01:22:53,638 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53fe7d6 - End of configuration. [testng] [2024-07-10 01:22:53,647] [pool-1-thread-9] Initializing /data/brian/images/raw_a.bmp: [testng] 01:22:53,647 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:22:53,647 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:53,648 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-10_01-22-53.log] [testng] 01:22:53,648 |-INFO in ch.qos.logback.core.sift.SiftProcessor@191d818a - End of configuration. [testng] [2024-07-10 01:22:53,657] [pool-1-thread-8] Initializing /data/brian/images/23srp5dksub.bmp: [testng] 01:22:53,658 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:22:53,658 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:53,659 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-10_01-22-53.log] [testng] 01:22:53,659 |-INFO in ch.qos.logback.core.sift.SiftProcessor@320a030b - End of configuration. [testng] [2024-07-10 01:22:53,672] [pool-1-thread-7] Initializing /data/qa-4538/22577136_Figure 2_A_ATF6 (GST)_13572.bmp: [testng] 01:22:53,672 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:22:53,672 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:53,673 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-10_01-22-53.log] [testng] 01:22:53,674 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d9d9c21 - End of configuration. [testng] [2024-07-10 01:22:53,686] [pool-1-thread-6] Initializing /data/dennis/kidney_TFl_Two.bmp: [testng] 01:22:53,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:22:53,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:53,688 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-10_01-22-53.log] [testng] 01:22:53,688 |-INFO in ch.qos.logback.core.sift.SiftProcessor@eedbd9b - End of configuration. [testng] [2024-07-10 01:22:53,702] [pool-1-thread-5] Initializing /data/curtis/image1.bmp: [testng] 01:22:53,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:22:53,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:53,703 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-10_01-22-53.log] [testng] 01:22:53,704 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42092bac - End of configuration. [testng] [2024-07-10 01:22:53,709] [pool-1-thread-4] Initializing /data/big-images/8kx8k-grey.bmp: [testng] 01:22:53,709 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:22:53,710 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:53,710 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-10_01-22-53.log] [testng] 01:22:53,711 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b016e2f - End of configuration. [testng] [2024-07-10 01:22:53,722] [pool-1-thread-3] Initializing /data/dennis/kidney_TFl_Seven.bmp: [testng] 01:22:53,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:22:53,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:53,724 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-10_01-22-53.log] [testng] 01:22:53,724 |-INFO in ch.qos.logback.core.sift.SiftProcessor@739576fe - End of configuration. [testng] [2024-07-10 01:22:53,734] [pool-1-thread-2] Initializing /data/dennis/kidney_TFl_Four.bmp: [testng] 01:22:53,735 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:22:53,735 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:53,736 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-10_01-22-53.log] [testng] 01:22:53,736 |-INFO in ch.qos.logback.core.sift.SiftProcessor@458fbe7f - End of configuration. [testng] [2024-07-10 01:22:54,893] [pool-1-thread-11] Initializing /data/brian/images/raw_a_rg.bmp: [testng] [2024-07-10 01:22:54,900] [pool-1-thread-5] Initializing /data/brian/images/raw_a_rg.tiff: [testng] [2024-07-10 01:22:54,929] [pool-1-thread-9] Initializing /data/brian/images/kidney_TFl_1_greyscale.bmp: [testng] [2024-07-10 01:22:54,936] [pool-1-thread-10] Initializing /data/stephane/holo0908.bmp: [testng] [2024-07-10 01:22:55,026] [pool-1-thread-3] Initializing /data/dennis/kidney_TFl_Eight.bmp: [testng] [2024-07-10 01:22:55,239] [pool-1-thread-2] Initializing /data/brian/images/DMSOHigh_001.bmp: [testng] [2024-07-10 01:22:55,246] [pool-1-thread-6] Initializing /data/curtis/image3.bmp: [testng] [2024-07-10 01:22:55,252] [pool-1-thread-8] Initializing /data/frank/cell_mask_error.bmp: [testng] [2024-07-10 01:22:55,311] [pool-1-thread-1] Initializing /data/curtis/image2.bmp: [testng] [2024-07-10 01:22:55,352] [pool-1-thread-9] Initializing /data/big-images/8kx8k.bmp: [testng] [2024-07-10 01:22:55,399] [pool-1-thread-11] Initializing /data/curtis/image4.bmp: [testng] [2024-07-10 01:22:55,487] [pool-1-thread-1] Initializing /data/bk/100427RBTLPC_FD3__A___5_T_001_ch_00_image_00025_Z_001.bmp: [testng] [2024-07-10 01:22:55,493] [pool-1-thread-3] Initializing /data/dennis/kidney_TFl_Five.bmp: [testng] [2024-07-10 01:22:55,541] [pool-1-thread-6] Initializing /data/curtis/image5.bmp: [testng] [2024-07-10 01:22:55,565] [pool-1-thread-5] Initializing /data/brian/images/kidney_TFl_1.bmp: [testng] [2024-07-10 01:22:55,638] [pool-1-thread-7] Initializing /data/dennis/kidney_TFl_Nine.bmp: [testng] [2024-07-10 01:22:55,643] [pool-1-thread-11] Initializing /data/dennis/kidney_TFl_Six.bmp: [testng] [2024-07-10 01:22:55,646] [pool-1-thread-10] Initializing /data/dennis/kidney_TFl_One.bmp: [testng] [2024-07-10 01:22:55,681] [pool-1-thread-8] Initializing /data/big-images/6kx6k-grey.bmp: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1643, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 28 seconds Finished: SUCCESS