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Started by upstream project "BIOFORMATS-test-repo" build number 10 originally caused by: Started by upstream project "Trigger" build number 13 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins1903509056838958411.sh + '[' imagepro = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_1604_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] 02:35:12,309 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:35:12,311 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 02:35:12,311 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:35:12,313 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:35:12,313 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:35:12,314 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:35:12,314 |-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] 02:35:12,314 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:35:12,315 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:35:12,316 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:35:12,317 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:35:12,317 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:35:12,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:35:12,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:35:12,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:35:12,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:35:12,538 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:35:12,539 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:35:12,539 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:35:12,540 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:35:12,540 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 02:35:12,541 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 02:35:12,541 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 226 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-24 02:35:12,551] [main] java.version = 17.0.2 [testng] 02:35:12,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:35:12,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:12,602 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-24_02-35-12.log] [testng] 02:35:12,604 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-03-24 02:35:12,606] [main] testng.directory = /data [testng] [2024-03-24 02:35:12,607] [main] testng.configDirectory = /config [testng] [2024-03-24 02:35:12,617] [main] testng.multiplier = 1.0 [testng] [2024-03-24 02:35:12,618] [main] testng.in-memory = false [testng] [2024-03-24 02:35:12,618] [main] testng.allow-missing = false [testng] [2024-03-24 02:35:12,618] [main] user.language = en [testng] [2024-03-24 02:35:12,618] [main] user.country = ${user.country} [testng] [2024-03-24 02:35:12,618] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-24 02:35:15,403] [main] ---------------------------------------- [testng] [2024-03-24 02:35:15,403] [main] Total files: 22 [testng] [2024-03-24 02:35:15,403] [main] Scan time: 2.785 s (126 ms/file) [testng] [2024-03-24 02:35:15,403] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-24 02:35:30,067] [pool-1-thread-1] Initializing /data/converted/mitosis-test.tif: [testng] 02:35:30,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:35:30,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:30,069 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-24_02-35-30.log] [testng] 02:35:30,069 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bdc3e0 - End of configuration. [testng] [2024-03-24 02:35:30,430] [pool-1-thread-12] Initializing /data/samples/TISSUE.TIF: [testng] 02:35:30,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:35:30,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:30,432 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-24_02-35-30.log] [testng] 02:35:30,432 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d9df37 - End of configuration. [testng] [2024-03-24 02:35:30,653] [pool-1-thread-11] Initializing /data/converted/NESb_C2_TP7.ipw: [testng] 02:35:30,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:35:30,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:30,654 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-24_02-35-30.log] [testng] 02:35:30,654 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ad6c9be - End of configuration. [testng] [2024-03-24 02:35:30,755] [pool-1-thread-10] Initializing /data/xiuwen/head2.seq: [testng] 02:35:30,755 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:35:30,755 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:30,756 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-24_02-35-30.log] [testng] 02:35:30,756 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d3126aa - End of configuration. [testng] [2024-03-24 02:35:30,943] [pool-1-thread-9] Initializing /data/converted/dub01.ipw: [testng] 02:35:30,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:35:30,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:30,944 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-24_02-35-30.log] [testng] 02:35:30,944 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14e48505 - End of configuration. [testng] [2024-03-24 02:35:31,085] [pool-1-thread-8] Initializing /data/converted/clown.ipw: [testng] 02:35:31,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:35:31,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:31,086 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-24_02-35-31.log] [testng] 02:35:31,087 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b3adad1 - End of configuration. [testng] [2024-03-24 02:35:31,197] [pool-1-thread-7] Initializing /data/converted/NESb_C2_TP7.seq: [testng] 02:35:31,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:35:31,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:31,198 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-24_02-35-31.log] [testng] 02:35:31,198 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d90057d - End of configuration. [testng] [2024-03-24 02:35:31,327] [pool-1-thread-6] Initializing /data/converted/clown8c.seq: [testng] 02:35:31,327 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:35:31,327 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:31,328 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-24_02-35-31.log] [testng] 02:35:31,328 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78ec7cc2 - End of configuration. [testng] [2024-03-24 02:35:31,452] [pool-1-thread-5] Initializing /data/converted/mitosis-test.ipw: [testng] 02:35:31,453 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:35:31,453 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:31,454 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-24_02-35-31.log] [testng] 02:35:31,454 |-INFO in ch.qos.logback.core.sift.SiftProcessor@243e9552 - End of configuration. [testng] [2024-03-24 02:35:31,587] [pool-1-thread-4] Initializing /data/converted/clown.tif: [testng] 02:35:31,587 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:35:31,587 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:31,588 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-24_02-35-31.log] [testng] 02:35:31,588 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53d9392d - End of configuration. [testng] [2024-03-24 02:35:31,689] [pool-1-thread-3] Initializing /data/converted/clown.seq: [testng] 02:35:31,689 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:35:31,689 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:31,690 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-24_02-35-31.log] [testng] 02:35:31,691 |-INFO in ch.qos.logback.core.sift.SiftProcessor@644add94 - End of configuration. [testng] [2024-03-24 02:35:31,799] [pool-1-thread-2] Initializing /data/converted/clown8c.tif: [testng] 02:35:31,799 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:35:31,799 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:31,800 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-24_02-35-31.log] [testng] 02:35:31,800 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3eb955da - End of configuration. [testng] [2024-03-24 02:35:34,450] [pool-1-thread-4] Initializing /data/converted/dub01.seq: [testng] [2024-03-24 02:35:34,563] [pool-1-thread-3] Initializing /data/samples/PROBE.TIF: [testng] [2024-03-24 02:35:34,665] [pool-1-thread-8] Initializing /data/converted/dub01.pic: [testng] [2024-03-24 02:35:34,757] [pool-1-thread-6] Initializing /data/converted/clown8c.ipw: [testng] [2024-03-24 02:35:34,942] [pool-1-thread-5] Initializing /data/alex/AFAset0003.ips: [testng] [2024-03-24 02:35:35,038] [pool-1-thread-9] Initializing /data/converted/mitosis-test.seq: [testng] [2024-03-24 02:35:35,302] [pool-1-thread-11] Initializing /data/samples/FLDUAL.TIF: [testng] [2024-03-24 02:35:35,565] [pool-1-thread-1] Initializing /data/samples/HEART.SEQ: [testng] [2024-03-24 02:35:35,704] [pool-1-thread-2] Initializing /data/converted/NESb_C2_TP7.tiff: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1113, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 1 minute 28 seconds Finished: SUCCESS