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Started by upstream project "BIOFORMATS-test-repo" build number 302 originally caused by: Started by upstream project "Trigger" build number 324 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins13790792652105026561.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_47862_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] 05:10:11,134 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 05:10:11,135 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 05:10:11,135 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:10:11,136 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:10:11,137 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 05:10:11,137 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 05:10:11,137 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 05:10:11,137 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:10:11,138 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:10:11,138 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 05:10:11,138 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 05:10:11,139 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 05:10:11,298 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 05:10:11,298 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 05:10:11,320 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 05:10:11,320 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 05:10:11,325 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 05:10:11,326 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 05:10:11,326 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 05:10:11,326 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 05:10:11,326 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 05:10:11,327 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 05:10:11,327 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 189 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-29 05:10:11,335] [main] java.version = 17.0.2 [testng] 05:10:11,338 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:10:11,338 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:10:11,377 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-29_05-10-11.log] [testng] 05:10:11,379 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-12-29 05:10:11,380] [main] testng.directory = /data [testng] [2024-12-29 05:10:11,381] [main] testng.configDirectory = /config [testng] [2024-12-29 05:10:11,389] [main] testng.multiplier = 1.0 [testng] [2024-12-29 05:10:11,390] [main] testng.in-memory = false [testng] [2024-12-29 05:10:11,390] [main] testng.allow-missing = false [testng] [2024-12-29 05:10:11,390] [main] user.language = en [testng] [2024-12-29 05:10:11,390] [main] user.country = ${user.country} [testng] [2024-12-29 05:10:11,390] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-29 05:10:15,749] [main] ---------------------------------------- [testng] [2024-12-29 05:10:15,749] [main] Total files: 32 [testng] [2024-12-29 05:10:15,749] [main] Scan time: 4.359 s (136 ms/file) [testng] [2024-12-29 05:10:15,750] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-29 05:10:55,610] [pool-1-thread-1] Initializing /data/qa-29459/bad.1sc: [testng] 05:10:55,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 05:10:55,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:10:55,612 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-29_05-10-55.log] [testng] 05:10:55,613 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e9b6d43 - End of configuration. [testng] [2024-12-29 05:10:56,293] [pool-1-thread-12] Initializing /data/qa-16880/c-src v7.1sc: [testng] 05:10:56,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 05:10:56,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:10:56,294 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-29_05-10-56.log] [testng] 05:10:56,294 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23205e60 - End of configuration. [testng] [2024-12-29 05:10:56,985] [pool-1-thread-11] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] 05:10:56,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 05:10:56,985 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:10:56,986 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-29_05-10-56.log] [testng] 05:10:56,986 |-INFO in ch.qos.logback.core.sift.SiftProcessor@70ce8a41 - End of configuration. [testng] [2024-12-29 05:10:59,446] [pool-1-thread-10] Initializing /data/keith/pg020410saur3.1sc: [testng] 05:10:59,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 05:10:59,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:10:59,447 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-29_05-10-59.log] [testng] 05:10:59,447 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63661626 - End of configuration. [testng] [2024-12-29 05:11:00,595] [pool-1-thread-9] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [testng] 05:11:00,595 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 05:11:00,595 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:11:00,596 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-29_05-11-00.log] [testng] 05:11:00,596 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26952479 - End of configuration. [testng] [2024-12-29 05:11:03,165] [pool-1-thread-8] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] 05:11:03,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 05:11:03,166 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:11:03,166 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-29_05-11-03.log] [testng] 05:11:03,166 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8d43452 - End of configuration. [testng] [2024-12-29 05:11:03,894] [pool-1-thread-7] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] 05:11:03,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 05:11:03,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:11:03,895 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-29_05-11-03.log] [testng] 05:11:03,895 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fc79eec - End of configuration. [testng] [2024-12-29 05:11:04,705] [pool-1-thread-6] Initializing /data/qa-29469/good.1sc: [testng] 05:11:04,705 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 05:11:04,705 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:11:04,706 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-29_05-11-04.log] [testng] 05:11:04,706 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60ad7c8f - End of configuration. [testng] [2024-12-29 05:11:05,378] [pool-1-thread-5] Initializing /data/qa-29459/bad.jpg: [testng] 05:11:05,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 05:11:05,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:11:05,379 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-29_05-11-05.log] [testng] 05:11:05,379 |-INFO in ch.qos.logback.core.sift.SiftProcessor@712bf5d7 - End of configuration. [testng] [2024-12-29 05:11:05,604] [pool-1-thread-4] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] 05:11:05,604 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 05:11:05,604 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:11:05,605 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-29_05-11-05.log] [testng] 05:11:05,606 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28e5f74f - End of configuration. [testng] [2024-12-29 05:11:06,433] [pool-1-thread-3] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] 05:11:06,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 05:11:06,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:11:06,434 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-29_05-11-06.log] [testng] 05:11:06,434 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1111d990 - End of configuration. [testng] [2024-12-29 05:11:09,566] [pool-1-thread-2] Initializing /data/geert/good example1.1sc.jpg: [testng] 05:11:09,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 05:11:09,567 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:11:09,568 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-29_05-11-09.log] [testng] 05:11:09,568 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4abe5db7 - End of configuration. [testng] [2024-12-29 05:11:17,029] [pool-1-thread-10] Initializing /data/keith/test2.1sc: [testng] [2024-12-29 05:11:17,748] [pool-1-thread-12] Initializing /data/adrian/test_img.1sc: [testng] [2024-12-29 05:11:18,396] [pool-1-thread-6] Initializing /data/sylvain/2009-10-26 14hr 59min: [testng] [2024-12-29 05:11:19,466] [pool-1-thread-5] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] [2024-12-29 05:11:21,790] [pool-1-thread-1] Initializing /data/keith/PF020426MRSA v2.1sc: [testng] [2024-12-29 05:11:22,481] [pool-1-thread-2] Initializing /data/geert/bad example1.1sc: [testng] [2024-12-29 05:11:23,726] [pool-1-thread-8] Initializing /data/samples/imagesEight.1sc: [testng] [2024-12-29 05:11:24,418] [pool-1-thread-7] Initializing /data/geert/bad example1.1sc.jpg: [testng] [2024-12-29 05:11:24,861] [pool-1-thread-4] Initializing /data/geert/bad example1.jpg: [testng] [2024-12-29 05:11:31,097] [pool-1-thread-10] Initializing /data/geert/good example1.1sc: [testng] [2024-12-29 05:11:31,989] [pool-1-thread-8] Initializing /data/qa-29469/bad2.1sc: [testng] [2024-12-29 05:11:32,761] [pool-1-thread-12] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] [2024-12-29 05:11:33,540] [pool-1-thread-1] Initializing /data/david/Original Biorad Gel format file.1sc: [testng] [2024-12-29 05:11:34,351] [pool-1-thread-2] Initializing /data/sylvain/2009-10-23 12hr 18min.tif: [testng] [2024-12-29 05:11:37,187] [pool-1-thread-6] Initializing /data/keith/PF020328saur v3.1sc: [testng] [2024-12-29 05:11:38,784] [pool-1-thread-3] Initializing /data/qa-29469/bad3.1sc: [testng] [2024-12-29 05:11:39,544] [pool-1-thread-11] Initializing /data/samples/Criterion.1sc: [testng] [2024-12-29 05:11:40,199] [pool-1-thread-7] Initializing /data/david/Opened in imageJ.tiff: [testng] [2024-12-29 05:11:42,538] [pool-1-thread-9] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] [2024-12-29 05:11:45,885] [pool-1-thread-4] Initializing /data/keith/test.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 55 seconds Finished: SUCCESS