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Started by upstream project "BIOFORMATS-test-repo" build number 243 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins16272920030555868646.sh + '[' imagepro = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_38326_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] 17:41:14,044 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 17:41:14,046 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 17:41:14,046 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 17:41:14,047 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 17:41:14,048 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 17:41:14,049 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 17:41:14,049 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 17:41:14,049 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 17:41:14,049 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 17:41:14,050 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 17:41:14,050 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 17:41:14,051 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 17:41:14,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 17:41:14,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 17:41:14,242 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 17:41:14,242 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 17:41:14,248 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 17:41:14,248 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 17:41:14,248 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 17:41:14,248 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 17:41:14,248 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 17:41:14,249 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 17:41:14,249 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 200 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-02 17:41:14,258] [main] java.version = 11.0.16 [testng] 17:41:14,261 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 17:41:14,261 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:41:14,303 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-02_17-41-14.log] [testng] 17:41:14,304 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-11-02 17:41:14,306] [main] testng.directory = /data [testng] [2024-11-02 17:41:14,306] [main] testng.configDirectory = /config [testng] [2024-11-02 17:41:14,315] [main] testng.multiplier = 1.0 [testng] [2024-11-02 17:41:14,317] [main] testng.in-memory = false [testng] [2024-11-02 17:41:14,317] [main] testng.allow-missing = false [testng] [2024-11-02 17:41:14,317] [main] user.language = en [testng] [2024-11-02 17:41:14,317] [main] user.country = ${user.country} [testng] [2024-11-02 17:41:14,317] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-02 17:41:17,830] [main] ---------------------------------------- [testng] [2024-11-02 17:41:17,830] [main] Total files: 22 [testng] [2024-11-02 17:41:17,830] [main] Scan time: 3.513 s (159 ms/file) [testng] [2024-11-02 17:41:17,830] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-02 17:41:33,234] [pool-1-thread-1] Initializing /data/converted/clown8c.tif: [testng] 17:41:33,235 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 17:41:33,235 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:41:33,237 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-02_17-41-33.log] [testng] 17:41:33,237 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f50bac2 - End of configuration. [testng] [2024-11-02 17:41:34,042] [pool-1-thread-12] Initializing /data/alex/AFAset0003.ips: [testng] 17:41:34,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 17:41:34,043 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:41:34,044 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-02_17-41-34.log] [testng] 17:41:34,044 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2eccac63 - End of configuration. [testng] [2024-11-02 17:41:34,383] [pool-1-thread-11] Initializing /data/converted/clown8c.ipw: [testng] 17:41:34,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 17:41:34,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:41:34,384 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-02_17-41-34.log] [testng] 17:41:34,385 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e77f532 - End of configuration. [testng] [2024-11-02 17:41:34,712] [pool-1-thread-10] Initializing /data/converted/NESb_C2_TP7.seq: [testng] 17:41:34,712 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 17:41:34,712 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:41:34,713 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-02_17-41-34.log] [testng] 17:41:34,714 |-INFO in ch.qos.logback.core.sift.SiftProcessor@176b6f5e - End of configuration. [testng] [2024-11-02 17:41:35,053] [pool-1-thread-9] Initializing /data/converted/mitosis-test.tif: [testng] 17:41:35,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 17:41:35,054 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:41:35,054 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-02_17-41-35.log] [testng] 17:41:35,055 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61739d02 - End of configuration. [testng] [2024-11-02 17:41:36,006] [pool-1-thread-8] Initializing /data/converted/dub01.pic: [testng] 17:41:36,006 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 17:41:36,006 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:41:36,007 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-02_17-41-36.log] [testng] 17:41:36,007 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77e243ac - End of configuration. [testng] [2024-11-02 17:41:36,311] [pool-1-thread-7] Initializing /data/converted/dub01.ipw: [testng] 17:41:36,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 17:41:36,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:41:36,312 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-02_17-41-36.log] [testng] 17:41:36,312 |-INFO in ch.qos.logback.core.sift.SiftProcessor@358869f5 - End of configuration. [testng] [2024-11-02 17:41:36,641] [pool-1-thread-6] Initializing /data/converted/clown.ipw: [testng] 17:41:36,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 17:41:36,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:41:36,642 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-02_17-41-36.log] [testng] 17:41:36,642 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79869d92 - End of configuration. [testng] [2024-11-02 17:41:36,953] [pool-1-thread-5] Initializing /data/samples/PROBE.TIF: [testng] 17:41:36,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 17:41:36,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:41:36,954 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-02_17-41-36.log] [testng] 17:41:36,954 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36f276ed - End of configuration. [testng] [2024-11-02 17:41:37,311] [pool-1-thread-4] Initializing /data/converted/mitosis-test.seq: [testng] 17:41:37,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 17:41:37,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:41:37,312 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-02_17-41-37.log] [testng] 17:41:37,312 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60cb4eda - End of configuration. [testng] [2024-11-02 17:41:37,650] [pool-1-thread-3] Initializing /data/samples/TISSUE.TIF: [testng] 17:41:37,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 17:41:37,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:41:37,651 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-02_17-41-37.log] [testng] 17:41:37,651 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5eae2cd8 - End of configuration. [testng] [2024-11-02 17:41:38,456] [pool-1-thread-2] Initializing /data/samples/HEART.SEQ: [testng] 17:41:38,456 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 17:41:38,456 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:41:38,457 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-02_17-41-38.log] [testng] 17:41:38,457 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3324e708 - End of configuration. [testng] [2024-11-02 17:41:42,804] [pool-1-thread-11] Initializing /data/converted/NESb_C2_TP7.tiff: [testng] [2024-11-02 17:41:43,632] [pool-1-thread-6] Initializing /data/samples/FLDUAL.TIF: [testng] [2024-11-02 17:41:44,488] [pool-1-thread-5] Initializing /data/converted/NESb_C2_TP7.ipw: [testng] [2024-11-02 17:41:44,811] [pool-1-thread-4] Initializing /data/converted/dub01.seq: [testng] [2024-11-02 17:41:45,157] [pool-1-thread-2] Initializing /data/converted/clown8c.seq: [testng] [2024-11-02 17:41:45,565] [pool-1-thread-8] Initializing /data/xiuwen/head2.seq: [testng] [2024-11-02 17:41:45,995] [pool-1-thread-10] Initializing /data/converted/clown.tif: [testng] [2024-11-02 17:41:46,385] [pool-1-thread-7] Initializing /data/converted/mitosis-test.ipw: [testng] [2024-11-02 17:41:47,731] [pool-1-thread-3] 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: 2 minutes 12 seconds Finished: SUCCESS