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Started by upstream project "BIOFORMATS-test-repo" build number 83 originally caused by: Started by upstream project "Trigger" build number 93 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/jenkins11540631688875277960.sh + '[' bmp = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_12626_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] 01:23:07,797 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:23:07,798 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:23:07,798 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:23:07,799 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:23:07,800 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:23:07,800 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:23:07,801 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:23:07,801 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:23:07,801 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:23:07,802 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:23:07,802 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:23:07,802 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:23:07,971 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:23:07,971 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:23:07,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:23:07,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:23:08,001 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:23:08,001 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:23:08,001 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:23:08,001 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:23:08,001 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:23:08,002 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:23:08,002 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 201 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-05 01:23:08,012] [main] java.version = 17.0.2 [testng] 01:23:08,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:23:08,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:08,057 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-05_01-23-08.log] [testng] 01:23:08,059 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-06-05 01:23:08,061] [main] testng.directory = /data [testng] [2024-06-05 01:23:08,061] [main] testng.configDirectory = /config [testng] [2024-06-05 01:23:08,070] [main] testng.multiplier = 1.0 [testng] [2024-06-05 01:23:08,071] [main] testng.in-memory = false [testng] [2024-06-05 01:23:08,071] [main] testng.allow-missing = false [testng] [2024-06-05 01:23:08,071] [main] user.language = en [testng] [2024-06-05 01:23:08,071] [main] user.country = ${user.country} [testng] [2024-06-05 01:23:08,071] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-05 01:23:08,503] [main] ---------------------------------------- [testng] [2024-06-05 01:23:08,503] [main] Total files: 31 [testng] [2024-06-05 01:23:08,503] [main] Scan time: 0.432 s (13 ms/file) [testng] [2024-06-05 01:23:08,503] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 31 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-05 01:23:10,037] [pool-1-thread-1] Initializing /data/bk/ch_00.bmp: [testng] 01:23:10,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:23:10,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:10,040 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-05_01-23-10.log] [testng] 01:23:10,040 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2abad664 - End of configuration. [testng] [2024-06-05 01:23:10,056] [pool-1-thread-12] Initializing /data/big-images/6kx6k.bmp: [testng] 01:23:10,056 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:23:10,056 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:10,057 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-05_01-23-10.log] [testng] 01:23:10,058 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4fa7b410 - End of configuration. [testng] [2024-06-05 01:23:10,117] [pool-1-thread-11] Initializing /data/ticket-12971/foo.bmp: [testng] 01:23:10,117 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:23:10,117 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:10,118 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-05_01-23-10.log] [testng] 01:23:10,119 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4578b14a - End of configuration. [testng] [2024-06-05 01:23:10,125] [pool-1-thread-10] Initializing /data/dennis/kidney_TFl_Three.bmp: [testng] 01:23:10,125 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:23:10,125 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:10,126 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-05_01-23-10.log] [testng] 01:23:10,127 |-INFO in ch.qos.logback.core.sift.SiftProcessor@552a98e8 - End of configuration. [testng] [2024-06-05 01:23:10,134] [pool-1-thread-9] Initializing /data/brian/images/raw_a.bmp: [testng] 01:23:10,134 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:23:10,134 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:10,135 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-05_01-23-10.log] [testng] 01:23:10,135 |-INFO in ch.qos.logback.core.sift.SiftProcessor@98fffe3 - End of configuration. [testng] [2024-06-05 01:23:10,147] [pool-1-thread-8] Initializing /data/brian/images/23srp5dksub.bmp: [testng] 01:23:10,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:23:10,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:10,148 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-05_01-23-10.log] [testng] 01:23:10,149 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d31d19f - End of configuration. [testng] [2024-06-05 01:23:10,168] [pool-1-thread-7] Initializing /data/qa-4538/22577136_Figure 2_A_ATF6 (GST)_13572.bmp: [testng] 01:23:10,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:23:10,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:10,170 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-05_01-23-10.log] [testng] 01:23:10,170 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62823acf - End of configuration. [testng] [2024-06-05 01:23:10,183] [pool-1-thread-6] Initializing /data/dennis/kidney_TFl_Two.bmp: [testng] 01:23:10,184 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:23:10,184 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:10,184 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-05_01-23-10.log] [testng] 01:23:10,185 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74b2f251 - End of configuration. [testng] [2024-06-05 01:23:10,194] [pool-1-thread-5] Initializing /data/curtis/image1.bmp: [testng] 01:23:10,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:23:10,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:10,195 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-05_01-23-10.log] [testng] 01:23:10,195 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d608af5 - End of configuration. [testng] [2024-06-05 01:23:10,201] [pool-1-thread-4] Initializing /data/big-images/8kx8k-grey.bmp: [testng] 01:23:10,201 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:23:10,201 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:10,202 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-05_01-23-10.log] [testng] 01:23:10,202 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8993ec1 - End of configuration. [testng] [2024-06-05 01:23:10,211] [pool-1-thread-3] Initializing /data/dennis/kidney_TFl_Seven.bmp: [testng] 01:23:10,212 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:23:10,212 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:10,213 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-05_01-23-10.log] [testng] 01:23:10,213 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25f195f1 - End of configuration. [testng] [2024-06-05 01:23:10,220] [pool-1-thread-2] Initializing /data/dennis/kidney_TFl_Four.bmp: [testng] 01:23:10,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:23:10,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:10,222 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-05_01-23-10.log] [testng] 01:23:10,223 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60aae8bf - End of configuration. [testng] [2024-06-05 01:23:11,734] [pool-1-thread-5] Initializing /data/brian/images/raw_a_rg.bmp: [testng] [2024-06-05 01:23:11,739] [pool-1-thread-11] Initializing /data/curtis/image3.bmp: [testng] [2024-06-05 01:23:11,742] [pool-1-thread-9] Initializing /data/frank/cell_mask_error.bmp: [testng] [2024-06-05 01:23:11,747] [pool-1-thread-10] Initializing /data/brian/images/DMSOHigh_001.bmp: [testng] [2024-06-05 01:23:11,754] [pool-1-thread-2] Initializing /data/dennis/kidney_TFl_Eight.bmp: [testng] [2024-06-05 01:23:11,759] [pool-1-thread-6] Initializing /data/brian/images/raw_a_rg.tiff: [testng] [2024-06-05 01:23:11,785] [pool-1-thread-3] Initializing /data/brian/images/kidney_TFl_1_greyscale.bmp: [testng] [2024-06-05 01:23:11,790] [pool-1-thread-8] Initializing /data/stephane/holo0908.bmp: [testng] [2024-06-05 01:23:11,941] [pool-1-thread-1] Initializing /data/curtis/image2.bmp: [testng] [2024-06-05 01:23:12,091] [pool-1-thread-11] Initializing /data/big-images/8kx8k.bmp: [testng] [2024-06-05 01:23:12,100] [pool-1-thread-7] Initializing /data/bk/100427RBTLPC_FD3__A___5_T_001_ch_00_image_00025_Z_001.bmp: [testng] [2024-06-05 01:23:12,106] [pool-1-thread-5] Initializing /data/curtis/image4.bmp: [testng] [2024-06-05 01:23:12,340] [pool-1-thread-6] Initializing /data/dennis/kidney_TFl_Five.bmp: [testng] [2024-06-05 01:23:12,416] [pool-1-thread-1] Initializing /data/curtis/image5.bmp: [testng] [2024-06-05 01:23:12,460] [pool-1-thread-5] Initializing /data/brian/images/kidney_TFl_1.bmp: [testng] [2024-06-05 01:23:12,465] [pool-1-thread-3] Initializing /data/dennis/kidney_TFl_Nine.bmp: [testng] [2024-06-05 01:23:12,516] [pool-1-thread-9] Initializing /data/dennis/kidney_TFl_One.bmp: [testng] [2024-06-05 01:23:12,565] [pool-1-thread-2] Initializing /data/dennis/kidney_TFl_Six.bmp: [testng] [2024-06-05 01:23:12,599] [pool-1-thread-1] 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: 30 seconds Finished: SUCCESS