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Started by upstream project "BIOFORMATS-test-repo" build number 38 originally caused by: Started by upstream project "Trigger" build number 44 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/jenkins15870558826933890788.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_5354_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] 10:17:39,582 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 10:17:39,584 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 10:17:39,584 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:17:39,585 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:17:39,586 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 10:17:39,586 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 10:17:39,586 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 10:17:39,586 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:17:39,587 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:17:39,587 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 10:17:39,587 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 10:17:39,587 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 10:17:39,878 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 10:17:39,879 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 10:17:39,916 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 10:17:39,916 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 10:17:39,926 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 10:17:39,926 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 10:17:39,926 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 10:17:39,927 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 10:17:39,927 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 10:17:39,928 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 10:17:39,928 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 341 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-19 10:17:39,939] [main] java.version = 1.8.0_342 [testng] 10:17:39,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 10:17:39,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:17:39,996 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-19_10-17-39.log] [testng] 10:17:39,998 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-04-19 10:17:40,001] [main] testng.directory = /data [testng] [2024-04-19 10:17:40,002] [main] testng.configDirectory = /config [testng] [2024-04-19 10:17:40,017] [main] testng.multiplier = 1.0 [testng] [2024-04-19 10:17:40,018] [main] testng.in-memory = false [testng] [2024-04-19 10:17:40,018] [main] testng.allow-missing = false [testng] [2024-04-19 10:17:40,018] [main] user.language = en [testng] [2024-04-19 10:17:40,018] [main] user.country = ${user.country} [testng] [2024-04-19 10:17:40,018] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-04-19 10:17:41,048] [main] ---------------------------------------- [testng] [2024-04-19 10:17:41,048] [main] Total files: 32 [testng] [2024-04-19 10:17:41,048] [main] Scan time: 1.03 s (32 ms/file) [testng] [2024-04-19 10:17:41,048] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-19 10:17:44,729] [pool-1-thread-1] Initializing /data/keith/PF020328saur v3.1sc: [testng] 10:17:44,729 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 10:17:44,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:17:44,731 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-19_10-17-44.log] [testng] 10:17:44,731 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fbe6446 - End of configuration. [testng] [2024-04-19 10:17:44,755] [pool-1-thread-12] Initializing /data/geert/good example1.1sc.jpg: [testng] 10:17:44,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 10:17:44,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:17:44,757 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-19_10-17-44.log] [testng] 10:17:44,757 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78a81d77 - End of configuration. [testng] [2024-04-19 10:17:44,774] [pool-1-thread-11] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] 10:17:44,774 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 10:17:44,774 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:17:44,775 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-19_10-17-44.log] [testng] 10:17:44,775 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4de73650 - End of configuration. [testng] [2024-04-19 10:17:44,837] [pool-1-thread-10] Initializing /data/geert/good example1.1sc: [testng] 10:17:44,838 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 10:17:44,838 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:17:44,839 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-19_10-17-44.log] [testng] 10:17:44,839 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ef79a64 - End of configuration. [testng] [2024-04-19 10:17:44,904] [pool-1-thread-9] Initializing /data/qa-29469/bad3.1sc: [testng] 10:17:44,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 10:17:44,904 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:17:44,905 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-19_10-17-44.log] [testng] 10:17:44,905 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c9a508c - End of configuration. [testng] [2024-04-19 10:17:44,951] [pool-1-thread-8] Initializing /data/david/Opened in imageJ.tiff: [testng] 10:17:44,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 10:17:44,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:17:44,952 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-19_10-17-44.log] [testng] 10:17:44,953 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e9a62f3 - End of configuration. [testng] [2024-04-19 10:17:44,995] [pool-1-thread-7] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] 10:17:44,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 10:17:44,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:17:44,996 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-19_10-17-44.log] [testng] 10:17:44,997 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46316cd4 - End of configuration. [testng] [2024-04-19 10:17:45,059] [pool-1-thread-6] Initializing /data/qa-16880/c-src v7.1sc: [testng] 10:17:45,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 10:17:45,060 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:17:45,060 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-19_10-17-45.log] [testng] 10:17:45,061 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5595581d - End of configuration. [testng] [2024-04-19 10:17:45,085] [pool-1-thread-5] Initializing /data/keith/test2.1sc: [testng] 10:17:45,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 10:17:45,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:17:45,086 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-19_10-17-45.log] [testng] 10:17:45,086 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a2f5d6 - End of configuration. [testng] [2024-04-19 10:17:45,113] [pool-1-thread-4] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] 10:17:45,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 10:17:45,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:17:45,115 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-19_10-17-45.log] [testng] 10:17:45,116 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a7f36ef - End of configuration. [testng] [2024-04-19 10:17:45,149] [pool-1-thread-3] Initializing /data/keith/pg020410saur3.1sc: [testng] 10:17:45,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 10:17:45,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:17:45,150 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-19_10-17-45.log] [testng] 10:17:45,151 |-INFO in ch.qos.logback.core.sift.SiftProcessor@661e893c - End of configuration. [testng] [2024-04-19 10:17:45,168] [pool-1-thread-2] Initializing /data/keith/test.1sc: [testng] 10:17:45,168 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 10:17:45,168 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:17:45,169 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-19_10-17-45.log] [testng] 10:17:45,169 |-INFO in ch.qos.logback.core.sift.SiftProcessor@73a3aee7 - End of configuration. [testng] [2024-04-19 10:17:47,179] [pool-1-thread-1] Initializing /data/adrian/test_img.1sc: [testng] [2024-04-19 10:17:47,222] [pool-1-thread-3] Initializing /data/samples/Criterion.1sc: [testng] [2024-04-19 10:17:47,266] [pool-1-thread-5] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] [2024-04-19 10:17:47,343] [pool-1-thread-2] Initializing /data/sylvain/2009-10-26 14hr 59min: [testng] [2024-04-19 10:17:47,407] [pool-1-thread-6] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] [2024-04-19 10:17:47,442] [pool-1-thread-12] Initializing /data/qa-29459/bad.1sc: [testng] [2024-04-19 10:17:47,504] [pool-1-thread-8] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] [2024-04-19 10:17:47,556] [pool-1-thread-9] Initializing /data/geert/bad example1.1sc: [testng] [2024-04-19 10:17:47,678] [pool-1-thread-4] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [testng] [2024-04-19 10:17:47,968] [pool-1-thread-11] Initializing /data/qa-29459/bad.jpg: [testng] [2024-04-19 10:17:47,983] [pool-1-thread-7] Initializing /data/sylvain/2009-10-23 12hr 18min.tif: [testng] [2024-04-19 10:17:48,242] [pool-1-thread-10] Initializing /data/geert/bad example1.jpg: [testng] [2024-04-19 10:17:48,855] [pool-1-thread-11] Initializing /data/samples/imagesEight.1sc: [testng] [2024-04-19 10:17:49,282] [pool-1-thread-3] Initializing /data/qa-29469/bad2.1sc: [testng] [2024-04-19 10:17:49,477] [pool-1-thread-12] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] [2024-04-19 10:17:49,503] [pool-1-thread-6] Initializing /data/qa-29469/good.1sc: [testng] [2024-04-19 10:17:49,551] [pool-1-thread-8] Initializing /data/geert/bad example1.1sc.jpg: [testng] [2024-04-19 10:17:49,624] [pool-1-thread-11] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] [2024-04-19 10:17:49,755] [pool-1-thread-1] Initializing /data/david/Original Biorad Gel format file.1sc: [testng] [2024-04-19 10:17:49,831] [pool-1-thread-9] Initializing /data/keith/PF020426MRSA v2.1sc: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1696, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 14 seconds Finished: SUCCESS