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Started by upstream project "BIOFORMATS-test-repo" build number 268 originally caused by: Started by upstream project "Trigger" build number 291 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/jenkins10961722126601201769.sh + '[' imagepro = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_42426_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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 13:23:09,733 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 13:23:09,735 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 13:23:09,735 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 13:23:09,736 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 13:23:09,737 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 13:23:09,737 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 13:23:09,737 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 13:23:09,737 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 13:23:09,738 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 13:23:09,739 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 13:23:09,739 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 13:23:09,739 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 13:23:09,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 13:23:09,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 13:23:09,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 13:23:09,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 13:23:09,929 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 13:23:09,929 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 13:23:09,929 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 13:23:09,930 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 13:23:09,930 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 13:23:09,930 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 13:23:09,930 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 192 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-26 13:23:09,939] [main] java.version = 11.0.16 [testng] 13:23:09,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 13:23:09,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:23:09,982 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-26_13-23-09.log] [testng] 13:23:09,983 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-11-26 13:23:09,985] [main] testng.directory = /data [testng] [2024-11-26 13:23:09,985] [main] testng.configDirectory = /config [testng] [2024-11-26 13:23:09,994] [main] testng.multiplier = 1.0 [testng] [2024-11-26 13:23:09,996] [main] testng.in-memory = false [testng] [2024-11-26 13:23:09,996] [main] testng.allow-missing = false [testng] [2024-11-26 13:23:09,996] [main] user.language = en [testng] [2024-11-26 13:23:09,996] [main] user.country = ${user.country} [testng] [2024-11-26 13:23:09,996] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-26 13:23:14,202] [main] ---------------------------------------- [testng] [2024-11-26 13:23:14,202] [main] Total files: 22 [testng] [2024-11-26 13:23:14,202] [main] Scan time: 4.205 s (191 ms/file) [testng] [2024-11-26 13:23:14,202] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-26 13:23:32,919] [pool-1-thread-1] Initializing /data/converted/clown8c.tif: [testng] 13:23:32,920 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 13:23:32,920 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:23:32,922 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-26_13-23-32.log] [testng] 13:23:32,922 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38441797 - End of configuration. [testng] [2024-11-26 13:23:34,030] [pool-1-thread-12] Initializing /data/alex/AFAset0003.ips: [testng] 13:23:34,030 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 13:23:34,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:23:34,031 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-26_13-23-34.log] [testng] 13:23:34,032 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46eaab39 - End of configuration. [testng] [2024-11-26 13:23:34,448] [pool-1-thread-11] Initializing /data/converted/clown8c.ipw: [testng] 13:23:34,448 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 13:23:34,448 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:23:34,449 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-26_13-23-34.log] [testng] 13:23:34,449 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c7a370e - End of configuration. [testng] [2024-11-26 13:23:34,904] [pool-1-thread-10] Initializing /data/converted/NESb_C2_TP7.seq: [testng] 13:23:34,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 13:23:34,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:23:34,905 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-26_13-23-34.log] [testng] 13:23:34,906 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35e6aa83 - End of configuration. [testng] [2024-11-26 13:23:35,388] [pool-1-thread-9] Initializing /data/converted/mitosis-test.tif: [testng] 13:23:35,388 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 13:23:35,389 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:23:35,389 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-26_13-23-35.log] [testng] 13:23:35,390 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62134627 - End of configuration. [testng] [2024-11-26 13:23:36,655] [pool-1-thread-8] Initializing /data/converted/dub01.pic: [testng] 13:23:36,655 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 13:23:36,655 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:23:36,656 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-26_13-23-36.log] [testng] 13:23:36,656 |-INFO in ch.qos.logback.core.sift.SiftProcessor@404f8e6b - End of configuration. [testng] [2024-11-26 13:23:37,099] [pool-1-thread-7] Initializing /data/converted/dub01.ipw: [testng] 13:23:37,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 13:23:37,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:23:37,100 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-26_13-23-37.log] [testng] 13:23:37,100 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1aa24911 - End of configuration. [testng] [2024-11-26 13:23:37,541] [pool-1-thread-6] Initializing /data/converted/clown.ipw: [testng] 13:23:37,541 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 13:23:37,541 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:23:37,542 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-26_13-23-37.log] [testng] 13:23:37,542 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b9e178d - End of configuration. [testng] [2024-11-26 13:23:37,958] [pool-1-thread-5] Initializing /data/samples/PROBE.TIF: [testng] 13:23:37,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 13:23:37,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:23:37,959 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-26_13-23-37.log] [testng] 13:23:37,960 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47e7dc82 - End of configuration. [testng] [2024-11-26 13:23:38,404] [pool-1-thread-4] Initializing /data/converted/mitosis-test.seq: [testng] 13:23:38,404 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 13:23:38,404 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:23:38,405 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-26_13-23-38.log] [testng] 13:23:38,405 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6951e508 - End of configuration. [testng] [2024-11-26 13:23:38,858] [pool-1-thread-3] Initializing /data/samples/TISSUE.TIF: [testng] 13:23:38,858 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 13:23:38,858 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:23:38,859 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-26_13-23-38.log] [testng] 13:23:38,859 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c0015ab - End of configuration. [testng] [2024-11-26 13:23:39,910] [pool-1-thread-2] Initializing /data/samples/HEART.SEQ: [testng] 13:23:39,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 13:23:39,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:23:39,911 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-26_13-23-39.log] [testng] 13:23:39,912 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1dfa18 - End of configuration. [testng] [2024-11-26 13:23:45,731] [pool-1-thread-11] Initializing /data/converted/NESb_C2_TP7.tiff: [testng] [2024-11-26 13:23:46,904] [pool-1-thread-6] Initializing /data/converted/clown.tif: [testng] [2024-11-26 13:23:47,459] [pool-1-thread-4] Initializing /data/samples/FLDUAL.TIF: [testng] [2024-11-26 13:23:48,586] [pool-1-thread-8] Initializing /data/converted/NESb_C2_TP7.ipw: [testng] [2024-11-26 13:23:49,025] [pool-1-thread-5] Initializing /data/converted/dub01.seq: [testng] [2024-11-26 13:23:49,482] [pool-1-thread-7] Initializing /data/converted/clown8c.seq: [testng] [2024-11-26 13:23:49,963] [pool-1-thread-2] Initializing /data/xiuwen/head2.seq: [testng] [2024-11-26 13:23:50,503] [pool-1-thread-10] Initializing /data/converted/mitosis-test.ipw: [testng] [2024-11-26 13:23:53,074] [pool-1-thread-1] Initializing /data/converted/clown.seq: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1113, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 3 minutes 8 seconds Finished: SUCCESS