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Started by upstream project "BIOFORMATS-test-repo" build number 10 originally caused by: Started by upstream project "Trigger" build number 13 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins5915885101858382334.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_1580_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] 02:06:44,250 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:06:44,252 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 02:06:44,252 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:06:44,252 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:06:44,253 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:06:44,253 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:06:44,253 |-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] 02:06:44,253 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:06:44,254 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:06:44,255 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:06:44,255 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:06:44,255 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:06:44,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:06:44,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:06:44,469 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:06:44,469 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:06:44,475 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:06:44,475 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:06:44,475 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:06:44,476 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:06:44,476 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 02:06:44,476 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 02:06:44,476 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 222 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-24 02:06:44,486] [main] java.version = 17.0.2 [testng] 02:06:44,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:06:44,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:06:44,558 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-24_02-06-44.log] [testng] 02:06:44,560 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-03-24 02:06:44,562] [main] testng.directory = /data [testng] [2024-03-24 02:06:44,562] [main] testng.configDirectory = /config [testng] [2024-03-24 02:06:44,582] [main] testng.multiplier = 1.0 [testng] [2024-03-24 02:06:44,583] [main] testng.in-memory = false [testng] [2024-03-24 02:06:44,583] [main] testng.allow-missing = false [testng] [2024-03-24 02:06:44,583] [main] user.language = en [testng] [2024-03-24 02:06:44,583] [main] user.country = ${user.country} [testng] [2024-03-24 02:06:44,583] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-24 02:06:46,438] [main] ---------------------------------------- [testng] [2024-03-24 02:06:46,438] [main] Total files: 32 [testng] [2024-03-24 02:06:46,438] [main] Scan time: 1.855 s (57 ms/file) [testng] [2024-03-24 02:06:46,439] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-24 02:06:59,251] [pool-1-thread-1] Initializing /data/david/Opened in imageJ.tiff: [testng] 02:06:59,252 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:06:59,252 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:06:59,253 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-24_02-06-59.log] [testng] 02:06:59,254 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28de766a - End of configuration. [testng] [2024-03-24 02:06:59,961] [pool-1-thread-12] Initializing /data/keith/test2.1sc: [testng] 02:06:59,961 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:06:59,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:06:59,962 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-24_02-06-59.log] [testng] 02:06:59,963 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c2b3118 - End of configuration. [testng] [2024-03-24 02:07:00,198] [pool-1-thread-11] Initializing /data/keith/PF020328saur v3.1sc: [testng] 02:07:00,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:07:00,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:07:00,199 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-24_02-07-00.log] [testng] 02:07:00,200 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13724d1f - End of configuration. [testng] [2024-03-24 02:07:00,433] [pool-1-thread-10] Initializing /data/geert/bad example1.jpg: [testng] 02:07:00,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:07:00,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:07:00,434 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-24_02-07-00.log] [testng] 02:07:00,435 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ecc8472 - End of configuration. [testng] [2024-03-24 02:07:00,513] [pool-1-thread-9] Initializing /data/adrian/test_img.1sc: [testng] 02:07:00,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:07:00,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:07:00,514 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-24_02-07-00.log] [testng] 02:07:00,514 |-INFO in ch.qos.logback.core.sift.SiftProcessor@109f3fbb - End of configuration. [testng] [2024-03-24 02:07:00,772] [pool-1-thread-8] Initializing /data/geert/bad example1.1sc: [testng] 02:07:00,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:07:00,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:07:00,773 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-24_02-07-00.log] [testng] 02:07:00,773 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d059742 - End of configuration. [testng] [2024-03-24 02:07:01,020] [pool-1-thread-7] Initializing /data/geert/good example1.1sc: [testng] 02:07:01,021 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:07:01,021 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:07:01,021 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-24_02-07-01.log] [testng] 02:07:01,022 |-INFO in ch.qos.logback.core.sift.SiftProcessor@96d371b - End of configuration. [testng] [2024-03-24 02:07:01,251] [pool-1-thread-6] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] 02:07:01,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:07:01,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:07:01,252 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-24_02-07-01.log] [testng] 02:07:01,252 |-INFO in ch.qos.logback.core.sift.SiftProcessor@394b5868 - End of configuration. [testng] [2024-03-24 02:07:01,489] [pool-1-thread-5] Initializing /data/qa-16880/c-src v7.1sc: [testng] 02:07:01,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:07:01,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:07:01,490 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-24_02-07-01.log] [testng] 02:07:01,491 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3aae331d - End of configuration. [testng] [2024-03-24 02:07:01,753] [pool-1-thread-4] Initializing /data/keith/test.1sc: [testng] 02:07:01,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:07:01,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:07:01,754 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-24_02-07-01.log] [testng] 02:07:01,755 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46718697 - End of configuration. [testng] [2024-03-24 02:07:01,981] [pool-1-thread-3] Initializing /data/qa-29459/bad.1sc: [testng] 02:07:01,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:07:01,981 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:07:01,982 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-24_02-07-01.log] [testng] 02:07:01,982 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ad4f8d6 - End of configuration. [testng] [2024-03-24 02:07:02,191] [pool-1-thread-2] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] 02:07:02,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:07:02,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:07:02,192 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-24_02-07-02.log] [testng] 02:07:02,192 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27a885e3 - End of configuration. [testng] [2024-03-24 02:07:06,139] [pool-1-thread-11] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [testng] [2024-03-24 02:07:06,845] [pool-1-thread-8] Initializing /data/geert/bad example1.1sc.jpg: [testng] [2024-03-24 02:07:06,964] [pool-1-thread-9] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] [2024-03-24 02:07:07,156] [pool-1-thread-4] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] [2024-03-24 02:07:07,978] [pool-1-thread-12] Initializing /data/keith/PF020426MRSA v2.1sc: [testng] [2024-03-24 02:07:08,140] [pool-1-thread-10] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] [2024-03-24 02:07:08,971] [pool-1-thread-5] Initializing /data/david/Original Biorad Gel format file.1sc: [testng] [2024-03-24 02:07:09,154] [pool-1-thread-3] Initializing /data/sylvain/2009-10-26 14hr 59min: [testng] [2024-03-24 02:07:09,434] [pool-1-thread-6] Initializing /data/geert/good example1.1sc.jpg: [testng] [2024-03-24 02:07:09,556] [pool-1-thread-7] Initializing /data/keith/pg020410saur3.1sc: [testng] [2024-03-24 02:07:10,140] [pool-1-thread-1] Initializing /data/qa-29459/bad.jpg: [testng] [2024-03-24 02:07:10,964] [pool-1-thread-2] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] [2024-03-24 02:07:11,587] [pool-1-thread-12] Initializing /data/samples/imagesEight.1sc: [testng] [2024-03-24 02:07:11,811] [pool-1-thread-5] Initializing /data/samples/Criterion.1sc: [testng] [2024-03-24 02:07:12,070] [pool-1-thread-7] Initializing /data/sylvain/2009-10-23 12hr 18min.tif: [testng] [2024-03-24 02:07:13,056] [pool-1-thread-6] Initializing /data/qa-29469/good.1sc: [testng] [2024-03-24 02:07:13,267] [pool-1-thread-9] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] [2024-03-24 02:07:13,577] [pool-1-thread-3] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] [2024-03-24 02:07:14,398] [pool-1-thread-8] Initializing /data/qa-29469/bad2.1sc: [testng] [2024-03-24 02:07:14,731] [pool-1-thread-1] 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: 39 seconds Finished: SUCCESS