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Started by upstream project "BIOFORMATS-test-repo" build number 219 originally caused by: Started by upstream project "Trigger" build number 246 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins2675459723358228520.sh + '[' leica-tcs = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_34839_merge_ci -v /uod/idr/repos/curated/leica-tcs:/data -v /uod/idr-scratch/merge-ci/curated/leica-tcs:/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] 06:00:33,429 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 06:00:33,430 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 06:00:33,430 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:00:33,431 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:00:33,432 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 06:00:33,432 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 06:00:33,432 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 06:00:33,432 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:00:33,433 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:00:33,433 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 06:00:33,434 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 06:00:33,434 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 06:00:33,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 06:00:33,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 06:00:33,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 06:00:33,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 06:00:33,642 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 06:00:33,642 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 06:00:33,642 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 06:00:33,643 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 06:00:33,643 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 06:00:33,644 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 06:00:33,644 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 211 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-13 06:00:33,653] [main] java.version = 17.0.2 [testng] 06:00:33,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 06:00:33,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:00:33,700 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-13_06-00-33.log] [testng] 06:00:33,702 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-10-13 06:00:33,704] [main] testng.directory = /data [testng] [2024-10-13 06:00:33,705] [main] testng.configDirectory = /config [testng] [2024-10-13 06:00:33,714] [main] testng.multiplier = 1.0 [testng] [2024-10-13 06:00:33,715] [main] testng.in-memory = false [testng] [2024-10-13 06:00:33,715] [main] testng.allow-missing = false [testng] [2024-10-13 06:00:33,715] [main] user.language = en [testng] [2024-10-13 06:00:33,715] [main] user.country = ${user.country} [testng] [2024-10-13 06:00:33,715] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-13 06:01:09,049] [main] ---------------------------------------- [testng] [2024-10-13 06:01:09,050] [main] Total files: 944 [testng] [2024-10-13 06:01:09,050] [main] Scan time: 35.334 s (37 ms/file) [testng] [2024-10-13 06:01:09,050] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-13 06:02:55,519] [pool-1-thread-1] Initializing /data/stjude/AntoDayzerocy3GRP.tif: [testng] 06:02:55,520 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 06:02:55,520 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:02:55,521 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-13_06-02-55.log] [testng] 06:02:55,521 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e61af46 - End of configuration. [testng] [2024-10-13 06:02:57,316] [pool-1-thread-12] Initializing /data/brian/Series002_z00_ch00.tif: [testng] 06:02:57,316 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 06:02:57,316 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:02:57,316 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-13_06-02-57.log] [testng] 06:02:57,317 |-INFO in ch.qos.logback.core.sift.SiftProcessor@648de2ba - End of configuration. [testng] [2024-10-13 06:02:58,839] [pool-1-thread-11] Initializing /data/martin/Series028_z00_ch00.tif: [testng] 06:02:58,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 06:02:58,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:02:58,840 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-13_06-02-58.log] [testng] 06:02:58,840 |-INFO in ch.qos.logback.core.sift.SiftProcessor@326191 - End of configuration. [testng] [2024-10-13 06:03:01,996] [pool-1-thread-10] Initializing /data/stjude/AntoDay4dblmy2GRP.tif: [testng] 06:03:01,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 06:03:01,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:03:01,996 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-13_06-03-01.log] [testng] 06:03:01,997 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54977096 - End of configuration. [testng] [2024-10-13 06:03:04,547] [pool-1-thread-9] Initializing /data/brian/Series002_z01.tif: [testng] 06:03:04,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 06:03:04,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:03:04,548 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-13_06-03-04.log] [testng] 06:03:04,548 |-INFO in ch.qos.logback.core.sift.SiftProcessor@673b5110 - End of configuration. [testng] [2024-10-13 06:03:08,081] [pool-1-thread-8] Initializing /data/primate/Leica_Image.tif: [testng] 06:03:08,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 06:03:08,082 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:03:08,082 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-13_06-03-08.log] [testng] 06:03:08,082 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bd6dbb2 - End of configuration. [testng] [2024-10-13 06:03:10,378] [pool-1-thread-7] Initializing /data/stjude/AntoDayzerocy3OVP.tif: [testng] 06:03:10,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 06:03:10,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:03:10,379 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-13_06-03-10.log] [testng] 06:03:10,380 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b196d81 - End of configuration. [testng] [2024-10-13 06:03:13,120] [pool-1-thread-6] Initializing /data/stjude/Antoday1dblmysglGRP.tif: [testng] 06:03:13,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 06:03:13,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:03:13,121 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-13_06-03-13.log] [testng] 06:03:13,122 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a56bb7b - End of configuration. [testng] [2024-10-13 06:03:15,511] [pool-1-thread-5] Initializing /data/stjude/Antoday1dblcatsglGRP.tif: [testng] 06:03:15,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 06:03:15,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:03:15,512 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-13_06-03-15.log] [testng] 06:03:15,512 |-INFO in ch.qos.logback.core.sift.SiftProcessor@625b1366 - End of configuration. [testng] [2024-10-13 06:03:17,952] [pool-1-thread-4] Initializing /data/stjude/AntoDay4dblmyGRP.tif: [testng] 06:03:17,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 06:03:17,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:03:17,953 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-13_06-03-17.log] [testng] 06:03:17,953 |-INFO in ch.qos.logback.core.sift.SiftProcessor@337b7eba - End of configuration. [testng] [2024-10-13 06:03:20,347] [pool-1-thread-3] Initializing /data/stjude/AntoDay1dblGRP.tif: [testng] 06:03:20,347 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 06:03:20,347 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:03:20,348 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-13_06-03-20.log] [testng] 06:03:20,348 |-INFO in ch.qos.logback.core.sift.SiftProcessor@355fb2c1 - End of configuration. [testng] [2024-10-13 06:03:22,827] [pool-1-thread-2] Initializing /data/stjude/AntoDay1cy3/c01f0001.TIF: [testng] 06:03:22,828 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 06:03:22,828 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:03:22,828 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-13_06-03-22.log] [testng] 06:03:22,829 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b55955f - End of configuration. [testng] [2024-10-13 06:03:39,239] [pool-1-thread-2] Initializing /data/stjude/AntoDay4dblcatdataGRP.tif: [testng] [2024-10-13 06:03:42,662] [pool-1-thread-8] Initializing /data/stjude/Antoday1dblcat2dataGRP.tif: [testng] [2024-10-13 06:03:47,957] [pool-1-thread-9] Initializing /data/dave/series 35/042911_Series035_t00_z000_ch00.tif: [testng] 08:00:22,762 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 08:00:22,762 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:00:22,763 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-13_08-00-22.log] [testng] 08:00:22,763 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78422efb - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 795, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 119 minutes 54 seconds Finished: SUCCESS