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Started by upstream project "BIOFORMATS-test-repo" build number 240 originally caused by: Started by upstream project "Trigger" build number 265 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins17257150144330064792.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_37810_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings 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] 03:11:10,745 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:11:10,746 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 03:11:10,746 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:11:10,747 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:11:10,748 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:11:10,748 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:11:10,748 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 03:11:10,748 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:11:10,749 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:11:10,750 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:11:10,750 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:11:10,750 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:11:10,914 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:11:10,915 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:11:10,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:11:10,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:11:10,948 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:11:10,948 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:11:10,948 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:11:10,949 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:11:10,949 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 03:11:10,949 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 03:11:10,950 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 201 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-31 03:11:10,959] [main] java.version = 21 [testng] 03:11:10,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:11:10,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:11:11,003 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-31_03-11-10.log] [testng] 03:11:11,005 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-10-31 03:11:11,006] [main] testng.directory = /data [testng] [2024-10-31 03:11:11,006] [main] testng.configDirectory = /config [testng] [2024-10-31 03:11:11,015] [main] testng.multiplier = 1.0 [testng] [2024-10-31 03:11:11,016] [main] testng.in-memory = false [testng] [2024-10-31 03:11:11,016] [main] testng.allow-missing = false [testng] [2024-10-31 03:11:11,016] [main] user.language = en [testng] [2024-10-31 03:11:11,016] [main] user.country = ${user.country} [testng] [2024-10-31 03:11:11,016] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-31 03:11:14,202] [main] ---------------------------------------- [testng] [2024-10-31 03:11:14,202] [main] Total files: 32 [testng] [2024-10-31 03:11:14,203] [main] Scan time: 3.186 s (99 ms/file) [testng] [2024-10-31 03:11:14,203] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-31 03:11:38,824] [pool-1-thread-1] Initializing /data/qa-16880/c-src v7.1sc: [testng] 03:11:38,824 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:11:38,825 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:11:38,826 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-31_03-11-38.log] [testng] 03:11:38,827 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6cf78aa6 - End of configuration. [testng] [2024-10-31 03:11:39,320] [pool-1-thread-12] Initializing /data/david/Opened in imageJ.tiff: [testng] 03:11:39,321 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:11:39,321 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:11:39,322 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-31_03-11-39.log] [testng] 03:11:39,322 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e74c0a2 - End of configuration. [testng] [2024-10-31 03:11:40,895] [pool-1-thread-11] Initializing /data/qa-29459/bad.1sc: [testng] 03:11:40,895 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:11:40,895 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:11:40,896 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-31_03-11-40.log] [testng] 03:11:40,896 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d4e10d9 - End of configuration. [testng] [2024-10-31 03:11:41,368] [pool-1-thread-10] Initializing /data/keith/test2.1sc: [testng] 03:11:41,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:11:41,368 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:11:41,368 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-31_03-11-41.log] [testng] 03:11:41,369 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f40231a - End of configuration. [testng] [2024-10-31 03:11:41,839] [pool-1-thread-9] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] 03:11:41,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:11:41,840 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:11:41,840 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-31_03-11-41.log] [testng] 03:11:41,841 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2dff486a - End of configuration. [testng] [2024-10-31 03:11:42,339] [pool-1-thread-8] Initializing /data/geert/good example1.1sc: [testng] 03:11:42,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:11:42,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:11:42,340 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-31_03-11-42.log] [testng] 03:11:42,340 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d4f6e44 - End of configuration. [testng] [2024-10-31 03:11:42,867] [pool-1-thread-7] Initializing /data/keith/pg020410saur3.1sc: [testng] 03:11:42,868 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:11:42,868 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:11:42,868 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-31_03-11-42.log] [testng] 03:11:42,869 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bb792c6 - End of configuration. [testng] [2024-10-31 03:11:43,336] [pool-1-thread-6] Initializing /data/qa-29469/good.1sc: [testng] 03:11:43,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:11:43,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:11:43,337 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-31_03-11-43.log] [testng] 03:11:43,338 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7be1c089 - End of configuration. [testng] [2024-10-31 03:11:43,827] [pool-1-thread-5] Initializing /data/keith/test.1sc: [testng] 03:11:43,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:11:43,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:11:43,828 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-31_03-11-43.log] [testng] 03:11:43,828 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b790b9b - End of configuration. [testng] [2024-10-31 03:11:44,306] [pool-1-thread-4] Initializing /data/qa-29469/bad2.1sc: [testng] 03:11:44,306 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:11:44,306 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:11:44,307 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-31_03-11-44.log] [testng] 03:11:44,307 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c3035a2 - End of configuration. [testng] [2024-10-31 03:11:44,844] [pool-1-thread-3] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] 03:11:44,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:11:44,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:11:44,845 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-31_03-11-44.log] [testng] 03:11:44,845 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41cb5e43 - End of configuration. [testng] [2024-10-31 03:11:46,608] [pool-1-thread-2] Initializing /data/geert/bad example1.1sc.jpg: [testng] 03:11:46,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:11:46,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:11:46,609 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-31_03-11-46.log] [testng] 03:11:46,609 |-INFO in ch.qos.logback.core.sift.SiftProcessor@454c9ff1 - End of configuration. [testng] [2024-10-31 03:11:51,514] [pool-1-thread-7] Initializing /data/geert/good example1.1sc.jpg: [testng] [2024-10-31 03:11:51,730] [pool-1-thread-10] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] [2024-10-31 03:11:53,539] [pool-1-thread-5] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] [2024-10-31 03:11:55,324] [pool-1-thread-11] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] [2024-10-31 03:11:55,798] [pool-1-thread-1] Initializing /data/qa-29469/bad3.1sc: [testng] [2024-10-31 03:11:56,311] [pool-1-thread-8] Initializing /data/adrian/test_img.1sc: [testng] [2024-10-31 03:11:56,757] [pool-1-thread-9] Initializing /data/geert/bad example1.1sc: [testng] [2024-10-31 03:11:57,202] [pool-1-thread-6] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] [2024-10-31 03:11:57,655] [pool-1-thread-4] Initializing /data/samples/imagesEight.1sc: [testng] [2024-10-31 03:11:58,103] [pool-1-thread-2] Initializing /data/samples/Criterion.1sc: [testng] [2024-10-31 03:12:01,930] [pool-1-thread-4] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] [2024-10-31 03:12:03,601] [pool-1-thread-2] Initializing /data/sylvain/2009-10-23 12hr 18min.tif: [testng] [2024-10-31 03:12:05,208] [pool-1-thread-12] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [testng] [2024-10-31 03:12:06,793] [pool-1-thread-1] Initializing /data/geert/bad example1.jpg: [testng] [2024-10-31 03:12:06,966] [pool-1-thread-11] Initializing /data/qa-29459/bad.jpg: [testng] [2024-10-31 03:12:07,103] [pool-1-thread-6] Initializing /data/keith/PF020426MRSA v2.1sc: [testng] [2024-10-31 03:12:07,526] [pool-1-thread-3] Initializing /data/sylvain/2009-10-26 14hr 59min: [testng] [2024-10-31 03:12:08,018] [pool-1-thread-9] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] [2024-10-31 03:12:08,520] [pool-1-thread-8] Initializing /data/keith/PF020328saur v3.1sc: [testng] [2024-10-31 03:12:08,976] [pool-1-thread-7] Initializing /data/david/Original Biorad Gel format file.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 10 seconds Finished: SUCCESS