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Started by upstream project "BIOFORMATS-test-repo" build number 114 originally caused by: Started by upstream project "Trigger" build number 127 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@10 [BIOFORMATS-test-folder@10] $ /bin/bash -xe /tmp/jenkins7983945812996300225.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_17819_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] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 02:20:41,256 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:20:41,257 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 02:20:41,257 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:20:41,258 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:20:41,258 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:20:41,259 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:20:41,259 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:20:41,259 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:20:41,260 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:20:41,260 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:20:41,260 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:20:41,261 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:20:41,436 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:20:41,436 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:20:41,462 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:20:41,462 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:20:41,468 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:20:41,468 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:20:41,468 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:20:41,468 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:20:41,468 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 02:20:41,469 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 02:20:41,469 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 209 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-07 02:20:41,478] [main] java.version = 17.0.2 [testng] 02:20:41,482 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:20:41,482 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:41,525 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-07_02-20-41.log] [testng] 02:20:41,527 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-07-07 02:20:41,529] [main] testng.directory = /data [testng] [2024-07-07 02:20:41,529] [main] testng.configDirectory = /config [testng] [2024-07-07 02:20:41,539] [main] testng.multiplier = 1.0 [testng] [2024-07-07 02:20:41,540] [main] testng.in-memory = false [testng] [2024-07-07 02:20:41,540] [main] testng.allow-missing = false [testng] [2024-07-07 02:20:41,540] [main] user.language = en [testng] [2024-07-07 02:20:41,540] [main] user.country = ${user.country} [testng] [2024-07-07 02:20:41,540] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-07 02:20:42,426] [main] ---------------------------------------- [testng] [2024-07-07 02:20:42,426] [main] Total files: 32 [testng] [2024-07-07 02:20:42,427] [main] Scan time: 0.886 s (27 ms/file) [testng] [2024-07-07 02:20:42,427] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-07 02:20:45,505] [pool-1-thread-1] Initializing /data/david/Opened in imageJ.tiff: [testng] 02:20:45,505 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:20:45,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:45,507 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-07_02-20-45.log] [testng] 02:20:45,507 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5bfac634 - End of configuration. [testng] [2024-07-07 02:20:45,555] [pool-1-thread-12] Initializing /data/keith/test2.1sc: [testng] 02:20:45,556 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:20:45,556 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:45,557 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-07_02-20-45.log] [testng] 02:20:45,558 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ec6927b - End of configuration. [testng] [2024-07-07 02:20:45,580] [pool-1-thread-11] Initializing /data/keith/PF020328saur v3.1sc: [testng] 02:20:45,580 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:20:45,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:45,582 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-07_02-20-45.log] [testng] 02:20:45,582 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3728eac3 - End of configuration. [testng] [2024-07-07 02:20:45,597] [pool-1-thread-10] Initializing /data/geert/bad example1.jpg: [testng] 02:20:45,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:20:45,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:45,599 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-07_02-20-45.log] [testng] 02:20:45,599 |-INFO in ch.qos.logback.core.sift.SiftProcessor@486c0e67 - End of configuration. [testng] [2024-07-07 02:20:45,650] [pool-1-thread-9] Initializing /data/adrian/test_img.1sc: [testng] 02:20:45,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:20:45,651 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:45,651 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-07_02-20-45.log] [testng] 02:20:45,652 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d31e599 - End of configuration. [testng] [2024-07-07 02:20:45,683] [pool-1-thread-8] Initializing /data/geert/bad example1.1sc: [testng] 02:20:45,684 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:20:45,684 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:45,685 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-07_02-20-45.log] [testng] 02:20:45,685 |-INFO in ch.qos.logback.core.sift.SiftProcessor@124acfe5 - End of configuration. [testng] [2024-07-07 02:20:45,733] [pool-1-thread-7] Initializing /data/geert/good example1.1sc: [testng] 02:20:45,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:20:45,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:45,735 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-07_02-20-45.log] [testng] 02:20:45,736 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20b3b008 - End of configuration. [testng] [2024-07-07 02:20:45,784] [pool-1-thread-6] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] 02:20:45,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:20:45,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:45,786 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-07_02-20-45.log] [testng] 02:20:45,787 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a9ea571 - End of configuration. [testng] [2024-07-07 02:20:45,814] [pool-1-thread-5] Initializing /data/qa-16880/c-src v7.1sc: [testng] 02:20:45,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:20:45,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:45,815 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-07_02-20-45.log] [testng] 02:20:45,816 |-INFO in ch.qos.logback.core.sift.SiftProcessor@109f3fbb - End of configuration. [testng] [2024-07-07 02:20:45,846] [pool-1-thread-4] Initializing /data/keith/test.1sc: [testng] 02:20:45,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:20:45,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:45,849 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-07_02-20-45.log] [testng] 02:20:45,849 |-INFO in ch.qos.logback.core.sift.SiftProcessor@529be425 - End of configuration. [testng] [2024-07-07 02:20:45,878] [pool-1-thread-3] Initializing /data/qa-29459/bad.1sc: [testng] 02:20:45,878 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:20:45,878 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:45,879 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-07_02-20-45.log] [testng] 02:20:45,880 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f489524 - End of configuration. [testng] [2024-07-07 02:20:45,919] [pool-1-thread-2] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] 02:20:45,919 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:20:45,920 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:20:45,920 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-07_02-20-45.log] [testng] 02:20:45,921 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e00f3cb - End of configuration. [testng] [2024-07-07 02:20:47,864] [pool-1-thread-4] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [testng] [2024-07-07 02:20:47,909] [pool-1-thread-11] Initializing /data/keith/PF020426MRSA v2.1sc: [testng] [2024-07-07 02:20:47,929] [pool-1-thread-12] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] [2024-07-07 02:20:47,964] [pool-1-thread-1] Initializing /data/david/Original Biorad Gel format file.1sc: [testng] [2024-07-07 02:20:47,983] [pool-1-thread-5] Initializing /data/sylvain/2009-10-26 14hr 59min: [testng] [2024-07-07 02:20:48,003] [pool-1-thread-3] Initializing /data/geert/good example1.1sc.jpg: [testng] [2024-07-07 02:20:48,149] [pool-1-thread-9] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] [2024-07-07 02:20:48,212] [pool-1-thread-7] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] [2024-07-07 02:20:48,465] [pool-1-thread-10] Initializing /data/geert/bad example1.1sc.jpg: [testng] [2024-07-07 02:20:48,519] [pool-1-thread-6] Initializing /data/qa-29459/bad.jpg: [testng] [2024-07-07 02:20:48,531] [pool-1-thread-8] Initializing /data/keith/pg020410saur3.1sc: [testng] [2024-07-07 02:20:48,840] [pool-1-thread-2] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] [2024-07-07 02:20:48,870] [pool-1-thread-11] Initializing /data/samples/imagesEight.1sc: [testng] [2024-07-07 02:20:48,928] [pool-1-thread-1] Initializing /data/samples/Criterion.1sc: [testng] [2024-07-07 02:20:49,113] [pool-1-thread-8] Initializing /data/sylvain/2009-10-23 12hr 18min.tif: [testng] [2024-07-07 02:20:49,387] [pool-1-thread-3] Initializing /data/qa-29469/good.1sc: [testng] [2024-07-07 02:20:49,455] [pool-1-thread-6] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] [2024-07-07 02:20:49,567] [pool-1-thread-5] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] [2024-07-07 02:20:49,684] [pool-1-thread-11] Initializing /data/qa-29469/bad2.1sc: [testng] [2024-07-07 02:20:49,736] [pool-1-thread-7] Initializing /data/qa-29469/bad3.1sc: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1696, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 15 seconds Finished: SUCCESS