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Started by upstream project "BIOFORMATS-test-repo" build number 30 originally caused by: Started by upstream project "Trigger" build number 33 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/jenkins10186732515614333443.sh + '[' leica-tcs = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_4051_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings 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] 02:34:00,241 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:34:00,243 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 02:34:00,243 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:34:00,244 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:34:00,244 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:34:00,245 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:34:00,245 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:34:00,245 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:34:00,245 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:34:00,246 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:34:00,246 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:34:00,247 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:34:00,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:34:00,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:34:00,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:34:00,460 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:34:00,467 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:34:00,467 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:34:00,467 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:34:00,467 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:34:00,468 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 02:34:00,468 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 02:34:00,468 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 223 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-11 02:34:00,478] [main] java.version = 21 [testng] 02:34:00,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:34:00,482 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:34:00,533 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-11_02-34-00.log] [testng] 02:34:00,535 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-04-11 02:34:00,537] [main] testng.directory = /data [testng] [2024-04-11 02:34:00,537] [main] testng.configDirectory = /config [testng] [2024-04-11 02:34:00,546] [main] testng.multiplier = 1.0 [testng] [2024-04-11 02:34:00,547] [main] testng.in-memory = false [testng] [2024-04-11 02:34:00,547] [main] testng.allow-missing = false [testng] [2024-04-11 02:34:00,547] [main] user.language = en [testng] [2024-04-11 02:34:00,547] [main] user.country = ${user.country} [testng] [2024-04-11 02:34:00,547] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-04-11 02:34:11,772] [main] ---------------------------------------- [testng] [2024-04-11 02:34:11,772] [main] Total files: 944 [testng] [2024-04-11 02:34:11,772] [main] Scan time: 11.224 s (11 ms/file) [testng] [2024-04-11 02:34:11,773] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-11 02:34:41,724] [pool-1-thread-1] Initializing /data/stjude/AntoDayzerocy3OVP.tif: [testng] 02:34:41,724 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:34:41,724 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:34:41,726 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-11_02-34-41.log] [testng] 02:34:41,726 |-INFO in ch.qos.logback.core.sift.SiftProcessor@259c9f4 - End of configuration. [testng] [2024-04-11 02:34:41,793] [pool-1-thread-12] Initializing /data/brian/Series002_z01.tif: [testng] 02:34:41,793 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:34:41,793 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:34:41,794 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-11_02-34-41.log] [testng] 02:34:41,794 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fb7e7d - End of configuration. [testng] [2024-04-11 02:34:41,901] [pool-1-thread-11] Initializing /data/stjude/Antoday1dblmysglGRP.tif: [testng] 02:34:41,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:34:41,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:34:41,903 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-11_02-34-41.log] [testng] 02:34:41,903 |-INFO in ch.qos.logback.core.sift.SiftProcessor@16d1ed50 - End of configuration. [testng] [2024-04-11 02:34:41,971] [pool-1-thread-10] Initializing /data/martin/Series028_z00_ch00.tif: [testng] 02:34:41,971 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:34:41,971 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:34:41,972 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-11_02-34-41.log] [testng] 02:34:41,972 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71cc116e - End of configuration. [testng] [2024-04-11 02:34:42,011] [pool-1-thread-9] Initializing /data/stjude/AntoDay4dblcatdataGRP.tif: [testng] 02:34:42,011 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:34:42,011 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:34:42,012 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-11_02-34-42.log] [testng] 02:34:42,012 |-INFO in ch.qos.logback.core.sift.SiftProcessor@585d15fa - End of configuration. [testng] [2024-04-11 02:34:42,055] [pool-1-thread-8] Initializing /data/brian/Series002_z00_ch00.tif: [testng] 02:34:42,055 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:34:42,055 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:34:42,056 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-11_02-34-42.log] [testng] 02:34:42,056 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2207a966 - End of configuration. [testng] [2024-04-11 02:34:42,091] [pool-1-thread-7] Initializing /data/primate/Leica_Image.tif: [testng] 02:34:42,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:34:42,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:34:42,093 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-11_02-34-42.log] [testng] 02:34:42,093 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4fb07359 - End of configuration. [testng] [2024-04-11 02:34:42,154] [pool-1-thread-6] Initializing /data/stjude/AntoDay4dblmy2GRP.tif: [testng] 02:34:42,155 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:34:42,155 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:34:42,156 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-11_02-34-42.log] [testng] 02:34:42,156 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c59eb6d - End of configuration. [testng] [2024-04-11 02:34:42,192] [pool-1-thread-5] Initializing /data/dave/series 35/042911_Series035_t00_z000_ch00.tif: [testng] 02:34:42,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:34:42,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:34:42,193 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-11_02-34-42.log] [testng] 02:34:42,193 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7348a1a1 - End of configuration. [testng] [2024-04-11 02:34:47,280] [pool-1-thread-4] Initializing /data/stjude/AntoDay4dblmyGRP.tif: [testng] 02:34:47,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:34:47,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:34:47,282 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-11_02-34-47.log] [testng] 02:34:47,282 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f307cac - End of configuration. [testng] [2024-04-11 02:34:47,324] [pool-1-thread-3] Initializing /data/stjude/AntoDayzerocy3GRP.tif: [testng] 02:34:47,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:34:47,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:34:47,325 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-11_02-34-47.log] [testng] 02:34:47,325 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3aa073d - End of configuration. [testng] [2024-04-11 02:34:47,357] [pool-1-thread-2] Initializing /data/stjude/AntoDay1dblGRP.tif: [testng] 02:34:47,357 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:34:47,357 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:34:47,358 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-11_02-34-47.log] [testng] 02:34:47,359 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d51cc2a - End of configuration. [testng] [2024-04-11 02:34:49,411] [pool-1-thread-2] Initializing /data/stjude/AntoDay1cy3/c01f0001.TIF: [testng] [2024-04-11 02:34:49,440] [pool-1-thread-12] Initializing /data/stjude/Antoday1dblcatsglGRP.tif: [testng] [2024-04-11 02:34:49,469] [pool-1-thread-10] Initializing /data/stjude/Antoday1dblcat2dataGRP.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 795, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 10 minutes 8 seconds Finished: SUCCESS