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Started by upstream project "BIOFORMATS-test-repo" build number 131 originally caused by: Started by upstream project "Trigger" build number 148 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/jenkins12112799874942262556.sh + '[' bmp = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_20498_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] 01:22:10,797 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:22:10,798 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:22:10,798 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:22:10,799 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:22:10,799 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:22:10,800 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:22:10,800 |-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] 01:22:10,800 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:22:10,800 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:22:10,801 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:22:10,801 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:22:10,802 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:22:10,984 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:22:10,984 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:22:11,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:22:11,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:22:11,026 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:22:11,027 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:22:11,027 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:22:11,028 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:22:11,028 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:22:11,029 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:22:11,029 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 229 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-24 01:22:11,042] [main] java.version = 17.0.2 [testng] 01:22:11,045 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:22:11,045 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:11,086 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-24_01-22-11.log] [testng] 01:22:11,092 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-07-24 01:22:11,095] [main] testng.directory = /data [testng] [2024-07-24 01:22:11,095] [main] testng.configDirectory = /config [testng] [2024-07-24 01:22:11,103] [main] testng.multiplier = 1.0 [testng] [2024-07-24 01:22:11,104] [main] testng.in-memory = false [testng] [2024-07-24 01:22:11,104] [main] testng.allow-missing = false [testng] [2024-07-24 01:22:11,105] [main] user.language = en [testng] [2024-07-24 01:22:11,105] [main] user.country = ${user.country} [testng] [2024-07-24 01:22:11,105] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-24 01:22:11,524] [main] ---------------------------------------- [testng] [2024-07-24 01:22:11,524] [main] Total files: 31 [testng] [2024-07-24 01:22:11,525] [main] Scan time: 0.419 s (13 ms/file) [testng] [2024-07-24 01:22:11,525] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 31 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-24 01:22:12,967] [pool-1-thread-1] Initializing /data/bk/ch_00.bmp: [testng] 01:22:12,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:22:12,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:12,970 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-24_01-22-12.log] [testng] 01:22:12,970 |-INFO in ch.qos.logback.core.sift.SiftProcessor@168c262f - End of configuration. [testng] [2024-07-24 01:22:12,987] [pool-1-thread-12] Initializing /data/big-images/6kx6k.bmp: [testng] 01:22:12,988 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:22:12,988 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:12,989 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-24_01-22-12.log] [testng] 01:22:12,989 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48dfc3f1 - End of configuration. [testng] [2024-07-24 01:22:13,013] [pool-1-thread-11] Initializing /data/ticket-12971/foo.bmp: [testng] 01:22:13,013 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:22:13,013 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:13,014 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-24_01-22-13.log] [testng] 01:22:13,014 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9fedd6a - End of configuration. [testng] [2024-07-24 01:22:13,021] [pool-1-thread-10] Initializing /data/dennis/kidney_TFl_Three.bmp: [testng] 01:22:13,021 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:22:13,021 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:13,022 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-24_01-22-13.log] [testng] 01:22:13,022 |-INFO in ch.qos.logback.core.sift.SiftProcessor@376902e6 - End of configuration. [testng] [2024-07-24 01:22:13,031] [pool-1-thread-9] Initializing /data/brian/images/raw_a.bmp: [testng] 01:22:13,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:22:13,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:13,032 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-24_01-22-13.log] [testng] 01:22:13,032 |-INFO in ch.qos.logback.core.sift.SiftProcessor@320a030b - End of configuration. [testng] [2024-07-24 01:22:13,072] [pool-1-thread-8] Initializing /data/brian/images/23srp5dksub.bmp: [testng] 01:22:13,073 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:22:13,073 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:13,074 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-24_01-22-13.log] [testng] 01:22:13,075 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d9d9c21 - End of configuration. [testng] [2024-07-24 01:22:13,105] [pool-1-thread-7] Initializing /data/qa-4538/22577136_Figure 2_A_ATF6 (GST)_13572.bmp: [testng] 01:22:13,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:22:13,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:13,106 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-24_01-22-13.log] [testng] 01:22:13,107 |-INFO in ch.qos.logback.core.sift.SiftProcessor@eedbd9b - End of configuration. [testng] [2024-07-24 01:22:13,133] [pool-1-thread-6] Initializing /data/dennis/kidney_TFl_Two.bmp: [testng] 01:22:13,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:22:13,133 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:13,136 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-24_01-22-13.log] [testng] 01:22:13,137 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42092bac - End of configuration. [testng] [2024-07-24 01:22:13,146] [pool-1-thread-5] Initializing /data/curtis/image1.bmp: [testng] 01:22:13,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:22:13,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:13,147 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-24_01-22-13.log] [testng] 01:22:13,148 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b016e2f - End of configuration. [testng] [2024-07-24 01:22:13,154] [pool-1-thread-4] Initializing /data/big-images/8kx8k-grey.bmp: [testng] 01:22:13,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:22:13,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:13,155 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-24_01-22-13.log] [testng] 01:22:13,155 |-INFO in ch.qos.logback.core.sift.SiftProcessor@739576fe - End of configuration. [testng] [2024-07-24 01:22:13,171] [pool-1-thread-3] Initializing /data/dennis/kidney_TFl_Seven.bmp: [testng] 01:22:13,171 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:22:13,171 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:13,184 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-24_01-22-13.log] [testng] 01:22:13,184 |-INFO in ch.qos.logback.core.sift.SiftProcessor@458fbe7f - End of configuration. [testng] [2024-07-24 01:22:13,191] [pool-1-thread-2] Initializing /data/dennis/kidney_TFl_Four.bmp: [testng] 01:22:13,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:22:13,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:22:13,192 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-24_01-22-13.log] [testng] 01:22:13,192 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54d53ac9 - End of configuration. [testng] [2024-07-24 01:22:14,190] [pool-1-thread-5] Initializing /data/brian/images/raw_a_rg.bmp: [testng] [2024-07-24 01:22:14,196] [pool-1-thread-11] Initializing /data/brian/images/kidney_TFl_1_greyscale.bmp: [testng] [2024-07-24 01:22:14,203] [pool-1-thread-9] Initializing /data/stephane/holo0908.bmp: [testng] [2024-07-24 01:22:14,535] [pool-1-thread-10] Initializing /data/brian/images/raw_a_rg.tiff: [testng] [2024-07-24 01:22:14,559] [pool-1-thread-3] Initializing /data/frank/cell_mask_error.bmp: [testng] [2024-07-24 01:22:14,565] [pool-1-thread-6] Initializing /data/brian/images/DMSOHigh_001.bmp: [testng] [2024-07-24 01:22:14,573] [pool-1-thread-2] Initializing /data/dennis/kidney_TFl_Eight.bmp: [testng] [2024-07-24 01:22:15,159] [pool-1-thread-8] Initializing /data/curtis/image3.bmp: [testng] [2024-07-24 01:22:15,163] [pool-1-thread-1] Initializing /data/curtis/image4.bmp: [testng] [2024-07-24 01:22:15,167] [pool-1-thread-11] Initializing /data/big-images/8kx8k.bmp: [testng] [2024-07-24 01:22:15,174] [pool-1-thread-5] Initializing /data/curtis/image2.bmp: [testng] [2024-07-24 01:22:15,325] [pool-1-thread-7] Initializing /data/bk/100427RBTLPC_FD3__A___5_T_001_ch_00_image_00025_Z_001.bmp: [testng] [2024-07-24 01:22:15,330] [pool-1-thread-3] Initializing /data/curtis/image5.bmp: [testng] [2024-07-24 01:22:15,334] [pool-1-thread-10] Initializing /data/dennis/kidney_TFl_Five.bmp: [testng] [2024-07-24 01:22:15,561] [pool-1-thread-5] Initializing /data/brian/images/kidney_TFl_1.bmp: [testng] [2024-07-24 01:22:15,565] [pool-1-thread-1] Initializing /data/dennis/kidney_TFl_One.bmp: [testng] [2024-07-24 01:22:15,569] [pool-1-thread-8] Initializing /data/dennis/kidney_TFl_Nine.bmp: [testng] [2024-07-24 01:22:15,586] [pool-1-thread-9] Initializing /data/dennis/kidney_TFl_Six.bmp: [testng] [2024-07-24 01:22:15,613] [pool-1-thread-2] 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: 35 seconds Finished: SUCCESS