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Started by upstream project "BIOFORMATS-test-repo" build number 227 originally caused by: Started by upstream project "Trigger" build number 252 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins18338751103895553809.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35677_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 test-automated: [testng] File leak detector installed [testng] 12:19:48,269 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 12:19:48,271 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 12:19:48,271 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:19:48,272 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:19:48,272 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 12:19:48,272 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 12:19:48,272 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 12:19:48,272 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:19:48,273 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:19:48,273 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 12:19:48,273 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 12:19:48,273 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 12:19:48,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 12:19:48,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 12:19:48,594 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 12:19:48,594 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 12:19:48,603 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 12:19:48,603 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 12:19:48,603 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 12:19:48,604 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 12:19:48,604 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 12:19:48,605 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 12:19:48,605 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 332 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-18 12:19:48,615] [main] java.version = 1.8.0_342 [testng] 12:19:48,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 12:19:48,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:19:48,723 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-18_12-19-48.log] [testng] 12:19:48,725 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-10-18 12:19:48,727] [main] testng.directory = /data [testng] [2024-10-18 12:19:48,727] [main] testng.configDirectory = /config [testng] [2024-10-18 12:19:48,739] [main] testng.multiplier = 1.0 [testng] [2024-10-18 12:19:48,740] [main] testng.in-memory = false [testng] [2024-10-18 12:19:48,740] [main] testng.allow-missing = false [testng] [2024-10-18 12:19:48,740] [main] user.language = en [testng] [2024-10-18 12:19:48,740] [main] user.country = ${user.country} [testng] [2024-10-18 12:19:48,740] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-18 12:19:52,619] [main] ---------------------------------------- [testng] [2024-10-18 12:19:52,620] [main] Total files: 32 [testng] [2024-10-18 12:19:52,620] [main] Scan time: 3.879 s (121 ms/file) [testng] [2024-10-18 12:19:52,620] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-18 12:20:18,656] [pool-1-thread-1] Initializing /data/geert/good example1.1sc.jpg: [testng] 12:20:18,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 12:20:18,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:20:18,657 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-18_12-20-18.log] [testng] 12:20:18,658 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e8c708b - End of configuration. [testng] [2024-10-18 12:20:18,838] [pool-1-thread-12] Initializing /data/geert/good example1.1sc: [testng] 12:20:18,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 12:20:18,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:20:18,839 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-18_12-20-18.log] [testng] 12:20:18,840 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ac0d593 - End of configuration. [testng] [2024-10-18 12:20:19,343] [pool-1-thread-11] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] 12:20:19,344 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 12:20:19,344 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:20:19,345 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-18_12-20-19.log] [testng] 12:20:19,345 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b2253e9 - End of configuration. [testng] [2024-10-18 12:20:19,835] [pool-1-thread-10] Initializing /data/geert/bad example1.jpg: [testng] 12:20:19,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 12:20:19,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:20:19,836 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-18_12-20-19.log] [testng] 12:20:19,837 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5bd0db88 - End of configuration. [testng] [2024-10-18 12:20:20,016] [pool-1-thread-9] Initializing /data/qa-29469/bad2.1sc: [testng] 12:20:20,016 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 12:20:20,016 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:20:20,017 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-18_12-20-20.log] [testng] 12:20:20,017 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47d0c5de - End of configuration. [testng] [2024-10-18 12:20:20,506] [pool-1-thread-8] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] 12:20:20,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 12:20:20,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:20:20,507 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-18_12-20-20.log] [testng] 12:20:20,507 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3af4a8f7 - End of configuration. [testng] [2024-10-18 12:20:22,176] [pool-1-thread-7] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] 12:20:22,176 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 12:20:22,176 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:20:22,177 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-18_12-20-22.log] [testng] 12:20:22,177 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c835c71 - End of configuration. [testng] [2024-10-18 12:20:22,679] [pool-1-thread-6] Initializing /data/keith/test2.1sc: [testng] 12:20:22,679 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 12:20:22,680 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:20:22,680 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-18_12-20-22.log] [testng] 12:20:22,681 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66d15b24 - End of configuration. [testng] [2024-10-18 12:20:23,167] [pool-1-thread-5] Initializing /data/keith/test.1sc: [testng] 12:20:23,167 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 12:20:23,167 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:20:23,167 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-18_12-20-23.log] [testng] 12:20:23,168 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d915af - End of configuration. [testng] [2024-10-18 12:20:23,684] [pool-1-thread-4] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] 12:20:23,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 12:20:23,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:20:23,685 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-18_12-20-23.log] [testng] 12:20:23,686 |-INFO in ch.qos.logback.core.sift.SiftProcessor@152a7cbe - End of configuration. [testng] [2024-10-18 12:20:25,455] [pool-1-thread-3] Initializing /data/keith/PF020426MRSA v2.1sc: [testng] 12:20:25,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 12:20:25,456 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:20:25,456 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-18_12-20-25.log] [testng] 12:20:25,457 |-INFO in ch.qos.logback.core.sift.SiftProcessor@272c00e8 - End of configuration. [testng] [2024-10-18 12:20:25,974] [pool-1-thread-2] Initializing /data/keith/pg020410saur3.1sc: [testng] 12:20:25,974 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 12:20:25,974 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:20:25,974 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-18_12-20-25.log] [testng] 12:20:25,975 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f457e49 - End of configuration. [testng] [2024-10-18 12:20:31,354] [pool-1-thread-2] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] [2024-10-18 12:20:33,161] [pool-1-thread-3] Initializing /data/qa-16880/c-src v7.1sc: [testng] [2024-10-18 12:20:33,636] [pool-1-thread-6] Initializing /data/adrian/test_img.1sc: [testng] [2024-10-18 12:20:34,131] [pool-1-thread-5] Initializing /data/david/Original Biorad Gel format file.1sc: [testng] [2024-10-18 12:20:34,565] [pool-1-thread-1] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] [2024-10-18 12:20:35,071] [pool-1-thread-9] Initializing /data/qa-29469/good.1sc: [testng] [2024-10-18 12:20:35,533] [pool-1-thread-11] Initializing /data/sylvain/2009-10-26 14hr 59min: [testng] [2024-10-18 12:20:36,005] [pool-1-thread-7] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] [2024-10-18 12:20:37,513] [pool-1-thread-10] Initializing /data/sylvain/2009-10-23 12hr 18min.tif: [testng] [2024-10-18 12:20:39,120] [pool-1-thread-12] Initializing /data/qa-29459/bad.1sc: [testng] [2024-10-18 12:20:42,661] [pool-1-thread-5] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] [2024-10-18 12:20:43,256] [pool-1-thread-9] Initializing /data/geert/bad example1.1sc.jpg: [testng] [2024-10-18 12:20:43,471] [pool-1-thread-3] Initializing /data/samples/Criterion.1sc: [testng] [2024-10-18 12:20:43,987] [pool-1-thread-1] Initializing /data/qa-29459/bad.jpg: [testng] [2024-10-18 12:20:44,150] [pool-1-thread-6] Initializing /data/geert/bad example1.1sc: [testng] [2024-10-18 12:20:44,631] [pool-1-thread-11] Initializing /data/samples/imagesEight.1sc: [testng] [2024-10-18 12:20:45,098] [pool-1-thread-8] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [testng] [2024-10-18 12:20:46,614] [pool-1-thread-4] Initializing /data/qa-29469/bad3.1sc: [testng] [2024-10-18 12:20:47,053] [pool-1-thread-12] Initializing /data/david/Opened in imageJ.tiff: [testng] [2024-10-18 12:20:50,374] [pool-1-thread-9] Initializing /data/keith/PF020328saur v3.1sc: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1696, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 1 minute 18 seconds Finished: SUCCESS