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Started by upstream project "BIOFORMATS-test-repo" build number 274 originally caused by: Started by upstream project "Trigger" build number 295 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins9629475087700183281.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_43257_merge_ci -v /uod/idr/repos/curated/biorad-gel:/data -v /uod/idr-scratch/merge-ci/curated/biorad-gel:/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] 03:10:32,191 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:10:32,193 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 03:10:32,193 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:10:32,194 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:10:32,195 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:10:32,195 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:10:32,195 |-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] 03:10:32,195 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:10:32,196 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:10:32,196 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:10:32,197 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:10:32,197 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:10:32,367 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:10:32,367 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:10:32,389 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:10:32,389 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:10:32,395 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:10:32,395 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:10:32,395 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:10:32,395 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:10:32,395 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 03:10:32,396 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 03:10:32,396 |-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] [2024-11-30 03:10:32,405] [main] java.version = 11.0.16 [testng] 03:10:32,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:10:32,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:10:32,450 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-30_03-10-32.log] [testng] 03:10:32,452 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-11-30 03:10:32,454] [main] testng.directory = /data [testng] [2024-11-30 03:10:32,455] [main] testng.configDirectory = /config [testng] [2024-11-30 03:10:32,464] [main] testng.multiplier = 1.0 [testng] [2024-11-30 03:10:32,466] [main] testng.in-memory = false [testng] [2024-11-30 03:10:32,466] [main] testng.allow-missing = false [testng] [2024-11-30 03:10:32,466] [main] user.language = en [testng] [2024-11-30 03:10:32,466] [main] user.country = ${user.country} [testng] [2024-11-30 03:10:32,466] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-30 03:10:35,064] [main] ---------------------------------------- [testng] [2024-11-30 03:10:35,065] [main] Total files: 32 [testng] [2024-11-30 03:10:35,065] [main] Scan time: 2.598 s (81 ms/file) [testng] [2024-11-30 03:10:35,065] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-30 03:10:49,908] [pool-1-thread-1] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] 03:10:49,909 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:10:49,909 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:10:49,910 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-30_03-10-49.log] [testng] 03:10:49,911 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40f3e542 - End of configuration. [testng] [2024-11-30 03:10:50,807] [pool-1-thread-12] Initializing /data/keith/test.1sc: [testng] 03:10:50,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:10:50,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:10:50,808 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-30_03-10-50.log] [testng] 03:10:50,809 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2612e71a - End of configuration. [testng] [2024-11-30 03:10:51,047] [pool-1-thread-11] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [testng] 03:10:51,047 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:10:51,047 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:10:51,047 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-30_03-10-51.log] [testng] 03:10:51,048 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47105e5 - End of configuration. [testng] [2024-11-30 03:10:51,945] [pool-1-thread-10] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] 03:10:51,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:10:51,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:10:51,946 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-30_03-10-51.log] [testng] 03:10:51,946 |-INFO in ch.qos.logback.core.sift.SiftProcessor@336e1e6a - End of configuration. [testng] [2024-11-30 03:10:52,245] [pool-1-thread-9] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] 03:10:52,245 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:10:52,245 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:10:52,246 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-30_03-10-52.log] [testng] 03:10:52,246 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c3b607a - End of configuration. [testng] [2024-11-30 03:10:52,530] [pool-1-thread-8] Initializing /data/samples/Criterion.1sc: [testng] 03:10:52,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:10:52,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:10:52,530 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-30_03-10-52.log] [testng] 03:10:52,531 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76f3ce37 - End of configuration. [testng] [2024-11-30 03:10:52,797] [pool-1-thread-7] Initializing /data/david/Original Biorad Gel format file.1sc: [testng] 03:10:52,797 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:10:52,797 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:10:52,798 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-30_03-10-52.log] [testng] 03:10:52,798 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45c15676 - End of configuration. [testng] [2024-11-30 03:10:53,064] [pool-1-thread-6] Initializing /data/david/Opened in imageJ.tiff: [testng] 03:10:53,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:10:53,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:10:53,066 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-30_03-10-53.log] [testng] 03:10:53,066 |-INFO in ch.qos.logback.core.sift.SiftProcessor@699bdce1 - End of configuration. [testng] [2024-11-30 03:10:53,906] [pool-1-thread-5] Initializing /data/adrian/test_img.1sc: [testng] 03:10:53,906 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:10:53,906 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:10:53,907 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-30_03-10-53.log] [testng] 03:10:53,907 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71c83175 - End of configuration. [testng] [2024-11-30 03:10:54,181] [pool-1-thread-4] Initializing /data/qa-29469/bad2.1sc: [testng] 03:10:54,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:10:54,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:10:54,182 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-30_03-10-54.log] [testng] 03:10:54,182 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f38e7a0 - End of configuration. [testng] [2024-11-30 03:10:54,443] [pool-1-thread-3] Initializing /data/sylvain/2009-10-23 12hr 18min.tif: [testng] 03:10:54,443 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:10:54,443 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:10:54,444 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-30_03-10-54.log] [testng] 03:10:54,444 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a075a73 - End of configuration. [testng] [2024-11-30 03:10:55,352] [pool-1-thread-2] Initializing /data/qa-29459/bad.1sc: [testng] 03:10:55,352 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:10:55,352 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:10:55,353 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-30_03-10-55.log] [testng] 03:10:55,353 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bcddaab - End of configuration. [testng] [2024-11-30 03:10:59,662] [pool-1-thread-12] Initializing /data/geert/good example1.1sc: [testng] [2024-11-30 03:10:59,944] [pool-1-thread-7] Initializing /data/geert/bad example1.1sc: [testng] [2024-11-30 03:11:00,225] [pool-1-thread-2] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] [2024-11-30 03:11:00,526] [pool-1-thread-4] Initializing /data/qa-16880/c-src v7.1sc: [testng] [2024-11-30 03:11:00,781] [pool-1-thread-8] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] [2024-11-30 03:11:01,641] [pool-1-thread-5] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] [2024-11-30 03:11:02,505] [pool-1-thread-9] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] [2024-11-30 03:11:03,422] [pool-1-thread-10] Initializing /data/keith/PF020426MRSA v2.1sc: [testng] [2024-11-30 03:11:06,707] [pool-1-thread-10] Initializing /data/keith/pg020410saur3.1sc: [testng] [2024-11-30 03:11:07,145] [pool-1-thread-4] Initializing /data/qa-29459/bad.jpg: [testng] [2024-11-30 03:11:07,265] [pool-1-thread-1] Initializing /data/keith/PF020328saur v3.1sc: [testng] [2024-11-30 03:11:07,509] [pool-1-thread-3] Initializing /data/qa-29469/bad3.1sc: [testng] [2024-11-30 03:11:07,768] [pool-1-thread-2] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] [2024-11-30 03:11:08,090] [pool-1-thread-6] Initializing /data/keith/test2.1sc: [testng] [2024-11-30 03:11:08,388] [pool-1-thread-12] Initializing /data/geert/bad example1.1sc.jpg: [testng] [2024-11-30 03:11:08,504] [pool-1-thread-7] Initializing /data/samples/imagesEight.1sc: [testng] [2024-11-30 03:11:08,736] [pool-1-thread-11] Initializing /data/geert/good example1.1sc.jpg: [testng] [2024-11-30 03:11:10,370] [pool-1-thread-10] Initializing /data/geert/bad example1.jpg: [testng] [2024-11-30 03:11:11,374] [pool-1-thread-7] Initializing /data/qa-29469/good.1sc: [testng] [2024-11-30 03:11:11,732] [pool-1-thread-1] Initializing /data/sylvain/2009-10-26 14hr 59min: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1696, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 45 seconds Finished: SUCCESS