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Started by upstream project "BIOFORMATS-test-repo" build number 286 originally caused by: Started by upstream project "Trigger" build number 305 originally caused by: Started by timer 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/jenkins9841643464142033178.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_45227_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] 04:30:50,759 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 04:30:50,761 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 04:30:50,761 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:30:50,762 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:30:50,762 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 04:30:50,762 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 04:30:50,763 |-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] 04:30:50,763 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:30:50,763 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:30:50,764 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 04:30:50,764 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 04:30:50,764 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 04:30:50,919 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 04:30:50,920 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 04:30:50,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 04:30:50,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 04:30:50,945 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 04:30:50,945 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 04:30:50,945 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 04:30:50,946 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 04:30:50,946 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 04:30:50,946 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 04:30:50,946 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 183 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-10 04:30:50,955] [main] java.version = 11.0.16 [testng] 04:30:50,957 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:30:50,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:30:50,997 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-10_04-30-50.log] [testng] 04:30:50,999 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-12-10 04:30:51,000] [main] testng.directory = /data [testng] [2024-12-10 04:30:51,000] [main] testng.configDirectory = /config [testng] [2024-12-10 04:30:51,009] [main] testng.multiplier = 1.0 [testng] [2024-12-10 04:30:51,010] [main] testng.in-memory = false [testng] [2024-12-10 04:30:51,011] [main] testng.allow-missing = false [testng] [2024-12-10 04:30:51,011] [main] user.language = en [testng] [2024-12-10 04:30:51,011] [main] user.country = ${user.country} [testng] [2024-12-10 04:30:51,011] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-10 04:31:03,196] [main] ---------------------------------------- [testng] [2024-12-10 04:31:03,196] [main] Total files: 32 [testng] [2024-12-10 04:31:03,196] [main] Scan time: 12.185 s (380 ms/file) [testng] [2024-12-10 04:31:03,196] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-10 04:32:13,059] [pool-1-thread-1] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] 04:32:13,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 04:32:13,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:13,062 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-10_04-32-13.log] [testng] 04:32:13,062 |-INFO in ch.qos.logback.core.sift.SiftProcessor@aa8c250 - End of configuration. [testng] [2024-12-10 04:32:19,692] [pool-1-thread-12] Initializing /data/keith/test.1sc: [testng] 04:32:19,692 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 04:32:19,692 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:19,693 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-10_04-32-19.log] [testng] 04:32:19,694 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20b26b23 - End of configuration. [testng] [2024-12-10 04:32:21,015] [pool-1-thread-11] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [testng] 04:32:21,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 04:32:21,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:21,015 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-10_04-32-21.log] [testng] 04:32:21,016 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b55b86a - End of configuration. [testng] [2024-12-10 04:32:25,879] [pool-1-thread-10] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] 04:32:25,879 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 04:32:25,879 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:25,880 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-10_04-32-25.log] [testng] 04:32:25,880 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27edf96a - End of configuration. [testng] [2024-12-10 04:32:27,310] [pool-1-thread-9] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] 04:32:27,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 04:32:27,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:27,311 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-10_04-32-27.log] [testng] 04:32:27,312 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5dba1c00 - End of configuration. [testng] [2024-12-10 04:32:28,708] [pool-1-thread-8] Initializing /data/samples/Criterion.1sc: [testng] 04:32:28,709 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 04:32:28,709 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:28,710 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-10_04-32-28.log] [testng] 04:32:28,710 |-INFO in ch.qos.logback.core.sift.SiftProcessor@736114c1 - End of configuration. [testng] [2024-12-10 04:32:30,163] [pool-1-thread-7] Initializing /data/david/Original Biorad Gel format file.1sc: [testng] 04:32:30,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 04:32:30,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:30,164 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-10_04-32-30.log] [testng] 04:32:30,165 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e72595e - End of configuration. [testng] [2024-12-10 04:32:31,690] [pool-1-thread-6] Initializing /data/david/Opened in imageJ.tiff: [testng] 04:32:31,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:32:31,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:31,691 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-10_04-32-31.log] [testng] 04:32:31,692 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75459243 - End of configuration. [testng] [2024-12-10 04:32:36,684] [pool-1-thread-5] Initializing /data/adrian/test_img.1sc: [testng] 04:32:36,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 04:32:36,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:36,685 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-10_04-32-36.log] [testng] 04:32:36,686 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60e8ee3f - End of configuration. [testng] [2024-12-10 04:32:38,067] [pool-1-thread-4] Initializing /data/qa-29469/bad2.1sc: [testng] 04:32:38,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 04:32:38,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:38,067 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-10_04-32-38.log] [testng] 04:32:38,068 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a25037d - End of configuration. [testng] [2024-12-10 04:32:39,489] [pool-1-thread-3] Initializing /data/sylvain/2009-10-23 12hr 18min.tif: [testng] 04:32:39,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 04:32:39,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:39,490 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-10_04-32-39.log] [testng] 04:32:39,490 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18a60b9a - End of configuration. [testng] [2024-12-10 04:32:44,498] [pool-1-thread-2] Initializing /data/qa-29459/bad.1sc: [testng] 04:32:44,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:32:44,498 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:32:44,498 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-10_04-32-44.log] [testng] 04:32:44,499 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61aa8a0c - End of configuration. [testng] [2024-12-10 04:32:57,580] [pool-1-thread-12] Initializing /data/geert/good example1.1sc: [testng] [2024-12-10 04:32:58,982] [pool-1-thread-7] Initializing /data/qa-16880/c-src v7.1sc: [testng] [2024-12-10 04:33:00,416] [pool-1-thread-2] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] [2024-12-10 04:33:05,566] [pool-1-thread-4] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] [2024-12-10 04:33:10,703] [pool-1-thread-8] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] [2024-12-10 04:33:15,545] [pool-1-thread-5] Initializing /data/keith/PF020426MRSA v2.1sc: [testng] [2024-12-10 04:33:18,398] [pool-1-thread-9] Initializing /data/geert/bad example1.1sc: [testng] [2024-12-10 04:33:19,923] [pool-1-thread-10] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] [2024-12-10 04:33:32,729] [pool-1-thread-5] Initializing /data/keith/pg020410saur3.1sc: [testng] [2024-12-10 04:33:34,390] [pool-1-thread-9] Initializing /data/qa-29459/bad.jpg: [testng] [2024-12-10 04:33:34,843] [pool-1-thread-7] Initializing /data/keith/test2.1sc: [testng] [2024-12-10 04:33:36,317] [pool-1-thread-10] Initializing /data/qa-29469/bad3.1sc: [testng] [2024-12-10 04:33:37,723] [pool-1-thread-12] Initializing /data/keith/PF020328saur v3.1sc: [testng] [2024-12-10 04:33:39,204] [pool-1-thread-1] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] [2024-12-10 04:33:40,986] [pool-1-thread-3] Initializing /data/geert/bad example1.1sc.jpg: [testng] [2024-12-10 04:33:41,511] [pool-1-thread-6] Initializing /data/samples/imagesEight.1sc: [testng] [2024-12-10 04:33:42,891] [pool-1-thread-11] Initializing /data/geert/good example1.1sc.jpg: [testng] [2024-12-10 04:33:51,448] [pool-1-thread-9] Initializing /data/geert/bad example1.jpg: [testng] [2024-12-10 04:33:52,059] [pool-1-thread-5] Initializing /data/qa-29469/good.1sc: [testng] [2024-12-10 04:33:53,634] [pool-1-thread-7] 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: 3 minutes 18 seconds Finished: SUCCESS