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Started by upstream project "BIOFORMATS-test-repo" build number 114 originally caused by: Started by upstream project "Trigger" build number 127 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins4819989349005923409.sh + '[' imagepro = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_17843_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] 02:40:20,557 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:40:20,559 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 02:40:20,559 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:40:20,560 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:40:20,560 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:40:20,560 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:40:20,561 |-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] 02:40:20,561 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:40:20,561 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:40:20,562 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:40:20,562 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:40:20,562 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:40:20,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:40:20,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:40:20,744 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:40:20,744 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:40:20,749 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:40:20,749 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:40:20,749 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:40:20,750 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:40:20,750 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 02:40:20,751 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 02:40:20,751 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 190 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-07 02:40:20,761] [main] java.version = 17.0.2 [testng] 02:40:20,764 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:40:20,764 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:20,804 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-07_02-40-20.log] [testng] 02:40:20,806 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-07-07 02:40:20,808] [main] testng.directory = /data [testng] [2024-07-07 02:40:20,808] [main] testng.configDirectory = /config [testng] [2024-07-07 02:40:20,816] [main] testng.multiplier = 1.0 [testng] [2024-07-07 02:40:20,817] [main] testng.in-memory = false [testng] [2024-07-07 02:40:20,817] [main] testng.allow-missing = false [testng] [2024-07-07 02:40:20,817] [main] user.language = en [testng] [2024-07-07 02:40:20,817] [main] user.country = ${user.country} [testng] [2024-07-07 02:40:20,817] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-07 02:40:22,149] [main] ---------------------------------------- [testng] [2024-07-07 02:40:22,149] [main] Total files: 22 [testng] [2024-07-07 02:40:22,149] [main] Scan time: 1.331 s (60 ms/file) [testng] [2024-07-07 02:40:22,149] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-07 02:40:31,683] [pool-1-thread-1] Initializing /data/converted/mitosis-test.tif: [testng] 02:40:31,684 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:40:31,684 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:31,685 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-07_02-40-31.log] [testng] 02:40:31,685 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c7b9029 - End of configuration. [testng] [2024-07-07 02:40:31,932] [pool-1-thread-12] Initializing /data/samples/TISSUE.TIF: [testng] 02:40:31,932 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:40:31,932 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:31,933 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-07_02-40-31.log] [testng] 02:40:31,933 |-INFO in ch.qos.logback.core.sift.SiftProcessor@495f603 - End of configuration. [testng] [2024-07-07 02:40:31,967] [pool-1-thread-11] Initializing /data/converted/NESb_C2_TP7.ipw: [testng] 02:40:31,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:40:31,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:31,968 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-07_02-40-31.log] [testng] 02:40:31,969 |-INFO in ch.qos.logback.core.sift.SiftProcessor@343f447c - End of configuration. [testng] [2024-07-07 02:40:32,001] [pool-1-thread-10] Initializing /data/xiuwen/head2.seq: [testng] 02:40:32,001 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:40:32,001 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:32,002 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-07_02-40-32.log] [testng] 02:40:32,002 |-INFO in ch.qos.logback.core.sift.SiftProcessor@16f5f455 - End of configuration. [testng] [2024-07-07 02:40:32,099] [pool-1-thread-9] Initializing /data/converted/dub01.ipw: [testng] 02:40:32,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:40:32,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:32,100 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-07_02-40-32.log] [testng] 02:40:32,100 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56788ca9 - End of configuration. [testng] [2024-07-07 02:40:32,128] [pool-1-thread-8] Initializing /data/converted/clown.ipw: [testng] 02:40:32,128 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:40:32,128 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:32,129 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-07_02-40-32.log] [testng] 02:40:32,129 |-INFO in ch.qos.logback.core.sift.SiftProcessor@567f307 - End of configuration. [testng] [2024-07-07 02:40:32,143] [pool-1-thread-7] Initializing /data/converted/NESb_C2_TP7.seq: [testng] 02:40:32,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:40:32,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:32,144 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-07_02-40-32.log] [testng] 02:40:32,144 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31c2906c - End of configuration. [testng] [2024-07-07 02:40:32,172] [pool-1-thread-6] Initializing /data/converted/clown8c.seq: [testng] 02:40:32,172 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:40:32,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:32,174 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-07_02-40-32.log] [testng] 02:40:32,174 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3888386c - End of configuration. [testng] [2024-07-07 02:40:32,193] [pool-1-thread-5] Initializing /data/converted/mitosis-test.ipw: [testng] 02:40:32,193 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:40:32,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:32,194 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-07_02-40-32.log] [testng] 02:40:32,195 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32f7604 - End of configuration. [testng] [2024-07-07 02:40:32,244] [pool-1-thread-4] Initializing /data/converted/clown.tif: [testng] 02:40:32,244 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:40:32,244 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:32,245 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-07_02-40-32.log] [testng] 02:40:32,245 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ad238b1 - End of configuration. [testng] [2024-07-07 02:40:32,282] [pool-1-thread-3] Initializing /data/converted/clown.seq: [testng] 02:40:32,282 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:40:32,283 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:32,283 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-07_02-40-32.log] [testng] 02:40:32,284 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48ba7317 - End of configuration. [testng] [2024-07-07 02:40:32,298] [pool-1-thread-2] Initializing /data/converted/clown8c.tif: [testng] 02:40:32,298 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:40:32,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:32,299 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-07_02-40-32.log] [testng] 02:40:32,300 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15e80250 - End of configuration. [testng] [2024-07-07 02:40:35,351] [pool-1-thread-2] Initializing /data/converted/dub01.seq: [testng] [2024-07-07 02:40:35,375] [pool-1-thread-4] Initializing /data/samples/HEART.SEQ: [testng] [2024-07-07 02:40:35,408] [pool-1-thread-6] Initializing /data/converted/NESb_C2_TP7.tiff: [testng] [2024-07-07 02:40:35,476] [pool-1-thread-3] Initializing /data/samples/FLDUAL.TIF: [testng] [2024-07-07 02:40:35,518] [pool-1-thread-5] Initializing /data/samples/PROBE.TIF: [testng] [2024-07-07 02:40:35,535] [pool-1-thread-12] Initializing /data/converted/dub01.pic: [testng] [2024-07-07 02:40:35,565] [pool-1-thread-7] Initializing /data/converted/clown8c.ipw: [testng] [2024-07-07 02:40:35,576] [pool-1-thread-11] Initializing /data/alex/AFAset0003.ips: [testng] [2024-07-07 02:40:35,586] [pool-1-thread-1] Initializing /data/converted/mitosis-test.seq: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1113, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 35 seconds Finished: SUCCESS