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Started by upstream project "BIOFORMATS-test-repo" build number 298 originally caused by: Started by upstream project "Trigger" build number 320 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins17973028146797466399.sh + '[' imagepro = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_47226_merge_ci -v /uod/idr/repos/curated/imagepro:/data -v /uod/idr-scratch/merge-ci/curated/imagepro:/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] 06:12:34,039 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 06:12:34,041 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 06:12:34,041 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:12:34,042 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:12:34,042 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 06:12:34,042 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 06:12:34,042 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 06:12:34,042 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:12:34,043 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:12:34,043 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 06:12:34,044 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 06:12:34,044 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 06:12:34,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 06:12:34,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 06:12:34,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 06:12:34,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 06:12:34,223 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 06:12:34,223 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 06:12:34,223 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 06:12:34,224 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 06:12:34,224 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 06:12:34,224 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 06:12:34,224 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 181 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-25 06:12:34,233] [main] java.version = 17.0.2 [testng] 06:12:34,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 06:12:34,236 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:12:34,274 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-25_06-12-34.log] [testng] 06:12:34,275 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-12-25 06:12:34,277] [main] testng.directory = /data [testng] [2024-12-25 06:12:34,277] [main] testng.configDirectory = /config [testng] [2024-12-25 06:12:34,286] [main] testng.multiplier = 1.0 [testng] [2024-12-25 06:12:34,286] [main] testng.in-memory = false [testng] [2024-12-25 06:12:34,286] [main] testng.allow-missing = false [testng] [2024-12-25 06:12:34,286] [main] user.language = en [testng] [2024-12-25 06:12:34,286] [main] user.country = ${user.country} [testng] [2024-12-25 06:12:34,286] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-25 06:12:41,193] [main] ---------------------------------------- [testng] [2024-12-25 06:12:41,193] [main] Total files: 22 [testng] [2024-12-25 06:12:41,193] [main] Scan time: 6.906 s (313 ms/file) [testng] [2024-12-25 06:12:41,193] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-25 06:13:05,558] [pool-1-thread-1] Initializing /data/converted/NESb_C2_TP7.ipw: [testng] 06:13:05,559 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 06:13:05,559 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:13:05,560 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-25_06-13-05.log] [testng] 06:13:05,560 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33c93a56 - End of configuration. [testng] [2024-12-25 06:13:06,192] [pool-1-thread-12] Initializing /data/alex/AFAset0003.ips: [testng] 06:13:06,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 06:13:06,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:13:06,193 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-25_06-13-06.log] [testng] 06:13:06,193 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ef0c82a - End of configuration. [testng] [2024-12-25 06:13:06,827] [pool-1-thread-11] Initializing /data/converted/clown8c.tif: [testng] 06:13:06,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 06:13:06,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:13:06,828 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-25_06-13-06.log] [testng] 06:13:06,829 |-INFO in ch.qos.logback.core.sift.SiftProcessor@682f7479 - End of configuration. [testng] [2024-12-25 06:13:08,574] [pool-1-thread-10] Initializing /data/converted/mitosis-test.ipw: [testng] 06:13:08,574 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 06:13:08,574 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:13:08,575 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-25_06-13-08.log] [testng] 06:13:08,576 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2fbd4e66 - End of configuration. [testng] [2024-12-25 06:13:09,212] [pool-1-thread-9] Initializing /data/converted/clown.seq: [testng] 06:13:09,213 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 06:13:09,213 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:13:09,213 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-25_06-13-09.log] [testng] 06:13:09,214 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e6bf276 - End of configuration. [testng] [2024-12-25 06:13:09,894] [pool-1-thread-8] Initializing /data/samples/HEART.SEQ: [testng] 06:13:09,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 06:13:09,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:13:09,895 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-25_06-13-09.log] [testng] 06:13:09,895 |-INFO in ch.qos.logback.core.sift.SiftProcessor@261e4ae3 - End of configuration. [testng] [2024-12-25 06:13:10,599] [pool-1-thread-7] Initializing /data/converted/dub01.ipw: [testng] 06:13:10,599 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 06:13:10,599 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:13:10,600 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-25_06-13-10.log] [testng] 06:13:10,600 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f00f51e - End of configuration. [testng] [2024-12-25 06:13:11,224] [pool-1-thread-6] Initializing /data/converted/clown.tif: [testng] 06:13:11,224 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 06:13:11,224 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:13:11,225 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-25_06-13-11.log] [testng] 06:13:11,225 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1bbf2160 - End of configuration. [testng] [2024-12-25 06:13:11,874] [pool-1-thread-5] Initializing /data/samples/PROBE.TIF: [testng] 06:13:11,874 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 06:13:11,874 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:13:11,875 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-25_06-13-11.log] [testng] 06:13:11,876 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2178fc12 - End of configuration. [testng] [2024-12-25 06:13:12,558] [pool-1-thread-4] Initializing /data/converted/clown8c.ipw: [testng] 06:13:12,558 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 06:13:12,558 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:13:12,559 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-25_06-13-12.log] [testng] 06:13:12,559 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57e6d10c - End of configuration. [testng] [2024-12-25 06:13:13,196] [pool-1-thread-3] Initializing /data/converted/clown8c.seq: [testng] 06:13:13,196 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 06:13:13,196 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:13:13,197 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-25_06-13-13.log] [testng] 06:13:13,197 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6265941d - End of configuration. [testng] [2024-12-25 06:13:13,850] [pool-1-thread-2] Initializing /data/converted/dub01.pic: [testng] 06:13:13,850 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 06:13:13,850 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:13:13,853 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-25_06-13-13.log] [testng] 06:13:13,853 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f5d248 - End of configuration. [testng] [2024-12-25 06:13:21,244] [pool-1-thread-10] Initializing /data/samples/FLDUAL.TIF: [testng] [2024-12-25 06:13:22,887] [pool-1-thread-2] Initializing /data/xiuwen/head2.seq: [testng] [2024-12-25 06:13:23,676] [pool-1-thread-3] Initializing /data/converted/NESb_C2_TP7.tiff: [testng] [2024-12-25 06:13:25,388] [pool-1-thread-6] Initializing /data/converted/mitosis-test.tif: [testng] [2024-12-25 06:13:27,198] [pool-1-thread-9] Initializing /data/converted/NESb_C2_TP7.seq: [testng] [2024-12-25 06:13:27,909] [pool-1-thread-7] Initializing /data/samples/TISSUE.TIF: [testng] [2024-12-25 06:13:29,563] [pool-1-thread-5] Initializing /data/converted/mitosis-test.seq: [testng] [2024-12-25 06:13:30,277] [pool-1-thread-8] Initializing /data/converted/dub01.seq: [testng] [2024-12-25 06:13:30,954] [pool-1-thread-1] Initializing /data/converted/clown.ipw: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1113, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 4 minutes 37 seconds Finished: SUCCESS