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Started by upstream project "BIOFORMATS-test-repo" build number 18 originally caused by: Started by upstream project "Trigger" build number 21 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins175957081036560165.sh + '[' leica-scn = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_2229_merge_ci -v /uod/idr/repos/curated/leica-scn:/data -v /uod/idr-scratch/merge-ci/curated/leica-scn:/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] 02:20:25,977 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:20:25,978 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 02:20:25,978 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:20:25,979 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:20:25,979 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:20:25,979 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:20:25,980 |-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] 02:20:25,980 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:20:25,980 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:20:25,981 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:20:25,981 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:20:25,981 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:20:26,142 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:20:26,142 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:20:26,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:20:26,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:20:26,169 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:20:26,170 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:20:26,170 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:20:26,170 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:20:26,170 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 02:20:26,171 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 02:20:26,171 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 191 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-31 02:20:26,180] [main] java.version = 17.0.2 [testng] 02:20:26,183 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:20:26,183 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:26,223 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-31_02-20-26.log] [testng] 02:20:26,225 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-03-31 02:20:26,227] [main] testng.directory = /data [testng] [2024-03-31 02:20:26,227] [main] testng.configDirectory = /config [testng] [2024-03-31 02:20:26,235] [main] testng.multiplier = 1.0 [testng] [2024-03-31 02:20:26,236] [main] testng.in-memory = false [testng] [2024-03-31 02:20:26,236] [main] testng.allow-missing = false [testng] [2024-03-31 02:20:26,237] [main] user.language = en [testng] [2024-03-31 02:20:26,237] [main] user.country = ${user.country} [testng] [2024-03-31 02:20:26,237] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-31 02:20:40,780] [main] ---------------------------------------- [testng] [2024-03-31 02:20:40,781] [main] Total files: 12 [testng] [2024-03-31 02:20:40,781] [main] Scan time: 14.543 s (1211 ms/file) [testng] [2024-03-31 02:20:40,781] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 12 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-31 02:20:42,351] [pool-1-thread-1] Initializing /data/michael/collection_0000008286_2012-05-23 17_20_46 opened usig LOCI.tif: [testng] 02:20:42,352 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:20:42,352 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:42,353 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-31_02-20-42.log] [testng] 02:20:42,353 |-INFO in ch.qos.logback.core.sift.SiftProcessor@297574d3 - End of configuration. [testng] [2024-03-31 02:20:42,409] [pool-1-thread-12] Initializing /data/qa-10469/Slide_907790L_DAPI_Ki67.scn: [testng] 02:20:42,410 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:20:42,410 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:42,411 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-31_02-20-42.log] [testng] 02:20:42,411 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a6ee7ae - End of configuration. [testng] [2024-03-31 02:20:42,566] [pool-1-thread-11] Initializing /data/mihaela/UCLAD_0000000280_2011-02-10 13_32_55Z.scn: [testng] 02:20:42,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:20:42,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:42,568 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-31_02-20-42.log] [testng] 02:20:42,568 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c02175d - End of configuration. [testng] [2024-03-31 02:20:42,662] [pool-1-thread-10] Initializing /data/michael/collection_0000008286_2012-05-23 17_20_46.scn: [testng] 02:20:42,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:20:42,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:42,664 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-31_02-20-42.log] [testng] 02:20:42,665 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62623231 - End of configuration. [testng] [2024-03-31 02:20:42,798] [pool-1-thread-9] Initializing /data/qa-11049/HP15.4994_2015-04-28.scn: [testng] 02:20:42,799 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:20:42,799 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:42,801 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-31_02-20-42.log] [testng] 02:20:42,802 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b4c4e6 - End of configuration. [testng] [2024-03-31 02:20:42,986] [pool-1-thread-8] Initializing /data/qa-17671/132223-12_022a1963-b32e-467f-8242-b51a5295951f.SCN: [testng] 02:20:42,987 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:20:42,987 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:42,988 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-31_02-20-42.log] [testng] 02:20:42,992 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d76d7ce - End of configuration. [testng] [2024-03-31 02:20:43,094] [pool-1-thread-7] Initializing /data/michael/collection_0000008286_2012-05-23 17_20_46 fullresolution.jpg: [testng] 02:20:43,094 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:20:43,094 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:43,095 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-31_02-20-43.log] [testng] 02:20:43,096 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a37f068 - End of configuration. [testng] [2024-03-31 02:20:43,152] [pool-1-thread-6] Initializing /data/scott/Oral_Biology_13 (1).scn: [testng] 02:20:43,153 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:20:43,153 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:43,154 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-31_02-20-43.log] [testng] 02:20:43,155 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c7596c6 - End of configuration. [testng] [2024-03-31 02:20:43,543] [pool-1-thread-5] Initializing /data/public/openslide/Leica-2/Leica-2.scn: [testng] 02:20:43,544 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:20:43,544 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:43,546 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-31_02-20-43.log] [testng] 02:20:43,547 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c9a4ce9 - End of configuration. [testng] [2024-03-31 02:20:43,722] [pool-1-thread-4] Initializing /data/scott/ImageCollection_0000000418_2010-10-27 13_31_31Z.scn: [testng] 02:20:43,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:20:43,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:43,724 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-31_02-20-43.log] [testng] 02:20:43,724 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13654114 - End of configuration. [testng] [2024-03-31 02:20:43,848] [pool-1-thread-3] Initializing /data/public/openslide/Leica-1/Leica-1.scn: [testng] 02:20:43,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:20:43,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:43,850 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-31_02-20-43.log] [testng] 02:20:43,851 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29b20693 - End of configuration. [testng] [2024-03-31 02:20:43,996] [pool-1-thread-2] Initializing /data/public/openslide/Leica-3/Leica-3.scn: [testng] 02:20:43,997 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:20:43,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:44,000 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-31_02-20-44.log] [testng] 02:20:44,001 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7518d72 - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 636, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 1 minute 52 seconds Finished: SUCCESS