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Started by upstream project "BIOFORMATS-test-repo" build number 194 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins1559726205820477796.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_30782_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 14:23:14,547 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 14:23:14,548 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 14:23:14,548 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 14:23:14,549 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 14:23:14,549 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 14:23:14,550 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 14:23:14,550 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 14:23:14,550 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 14:23:14,551 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 14:23:14,551 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 14:23:14,551 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 14:23:14,552 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 14:23:14,719 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 14:23:14,719 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 14:23:14,744 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 14:23:14,744 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 14:23:14,750 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 14:23:14,750 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 14:23:14,750 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 14:23:14,751 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 14:23:14,751 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 14:23:14,751 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 14:23:14,751 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 200 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-19 14:23:14,760] [main] java.version = 21 [testng] 14:23:14,763 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 14:23:14,763 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:23:14,803 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-19_14-23-14.log] [testng] 14:23:14,804 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-09-19 14:23:14,806] [main] testng.directory = /data [testng] [2024-09-19 14:23:14,806] [main] testng.configDirectory = /config [testng] [2024-09-19 14:23:14,814] [main] testng.multiplier = 1.0 [testng] [2024-09-19 14:23:14,815] [main] testng.in-memory = false [testng] [2024-09-19 14:23:14,815] [main] testng.allow-missing = false [testng] [2024-09-19 14:23:14,815] [main] user.language = en [testng] [2024-09-19 14:23:14,815] [main] user.country = ${user.country} [testng] [2024-09-19 14:23:14,815] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-09-19 14:23:20,508] [main] ---------------------------------------- [testng] [2024-09-19 14:23:20,508] [main] Total files: 32 [testng] [2024-09-19 14:23:20,508] [main] Scan time: 5.693 s (177 ms/file) [testng] [2024-09-19 14:23:20,509] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-19 14:23:53,490] [pool-1-thread-1] Initializing /data/sylvain/2009-10-26 14hr 59min: [testng] 14:23:53,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 14:23:53,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:23:53,492 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-19_14-23-53.log] [testng] 14:23:53,492 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56ab459b - End of configuration. [testng] [2024-09-19 14:23:54,107] [pool-1-thread-12] Initializing /data/qa-29469/bad2.1sc: [testng] 14:23:54,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 14:23:54,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:23:54,108 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-19_14-23-54.log] [testng] 14:23:54,108 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e312ad6 - End of configuration. [testng] [2024-09-19 14:23:54,656] [pool-1-thread-11] Initializing /data/david/Opened in imageJ.tiff: [testng] 14:23:54,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 14:23:54,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:23:54,657 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-19_14-23-54.log] [testng] 14:23:54,657 |-INFO in ch.qos.logback.core.sift.SiftProcessor@264e3cf1 - End of configuration. [testng] [2024-09-19 14:23:56,884] [pool-1-thread-10] Initializing /data/keith/PF020426MRSA v2.1sc: [testng] 14:23:56,885 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 14:23:56,885 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:23:56,885 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-19_14-23-56.log] [testng] 14:23:56,886 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46e78431 - End of configuration. [testng] [2024-09-19 14:23:57,434] [pool-1-thread-9] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] 14:23:57,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 14:23:57,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:23:57,435 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-19_14-23-57.log] [testng] 14:23:57,435 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e73a547 - End of configuration. [testng] [2024-09-19 14:23:58,049] [pool-1-thread-8] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] 14:23:58,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 14:23:58,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:23:58,050 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-19_14-23-58.log] [testng] 14:23:58,050 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bb792c6 - End of configuration. [testng] [2024-09-19 14:24:00,076] [pool-1-thread-7] Initializing /data/david/Original Biorad Gel format file.1sc: [testng] 14:24:00,076 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 14:24:00,076 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:24:00,077 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-19_14-24-00.log] [testng] 14:24:00,077 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7be1c089 - End of configuration. [testng] [2024-09-19 14:24:00,643] [pool-1-thread-6] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] 14:24:00,643 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 14:24:00,643 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:24:00,644 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-19_14-24-00.log] [testng] 14:24:00,644 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b790b9b - End of configuration. [testng] [2024-09-19 14:24:01,309] [pool-1-thread-5] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] 14:24:01,310 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 14:24:01,310 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:24:01,310 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-19_14-24-01.log] [testng] 14:24:01,311 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c3035a2 - End of configuration. [testng] [2024-09-19 14:24:03,735] [pool-1-thread-4] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] 14:24:03,736 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 14:24:03,736 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:24:03,736 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-19_14-24-03.log] [testng] 14:24:03,737 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41cb5e43 - End of configuration. [testng] [2024-09-19 14:24:05,998] [pool-1-thread-3] Initializing /data/qa-29459/bad.1sc: [testng] 14:24:05,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 14:24:05,999 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:24:05,999 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-19_14-24-05.log] [testng] 14:24:05,999 |-INFO in ch.qos.logback.core.sift.SiftProcessor@454c9ff1 - End of configuration. [testng] [2024-09-19 14:24:06,841] [pool-1-thread-2] Initializing /data/qa-29459/bad.jpg: [testng] 14:24:06,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 14:24:06,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:24:06,842 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-19_14-24-06.log] [testng] 14:24:06,843 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50e527ef - End of configuration. [testng] [2024-09-19 14:24:13,219] [pool-1-thread-2] Initializing /data/keith/test.1sc: [testng] [2024-09-19 14:24:13,856] [pool-1-thread-10] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] [2024-09-19 14:24:14,463] [pool-1-thread-7] Initializing /data/keith/PF020328saur v3.1sc: [testng] [2024-09-19 14:24:15,135] [pool-1-thread-3] Initializing /data/sylvain/2009-10-23 12hr 18min.tif: [testng] [2024-09-19 14:24:17,555] [pool-1-thread-12] Initializing /data/keith/test2.1sc: [testng] [2024-09-19 14:24:18,112] [pool-1-thread-9] Initializing /data/samples/Criterion.1sc: [testng] [2024-09-19 14:24:18,764] [pool-1-thread-1] Initializing /data/geert/bad example1.1sc.jpg: [testng] [2024-09-19 14:24:19,055] [pool-1-thread-6] Initializing /data/geert/bad example1.1sc: [testng] [2024-09-19 14:24:24,326] [pool-1-thread-7] Initializing /data/geert/good example1.1sc.jpg: [testng] [2024-09-19 14:24:24,629] [pool-1-thread-12] Initializing /data/samples/imagesEight.1sc: [testng] [2024-09-19 14:24:25,408] [pool-1-thread-2] Initializing /data/qa-29469/bad3.1sc: [testng] [2024-09-19 14:24:26,051] [pool-1-thread-9] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] [2024-09-19 14:24:28,084] [pool-1-thread-10] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [testng] [2024-09-19 14:24:30,770] [pool-1-thread-6] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] [2024-09-19 14:24:31,645] [pool-1-thread-11] Initializing /data/qa-16880/c-src v7.1sc: [testng] [2024-09-19 14:24:32,471] [pool-1-thread-8] Initializing /data/geert/bad example1.jpg: [testng] [2024-09-19 14:24:32,740] [pool-1-thread-5] Initializing /data/keith/pg020410saur3.1sc: [testng] [2024-09-19 14:24:33,292] [pool-1-thread-4] Initializing /data/qa-29469/good.1sc: [testng] [2024-09-19 14:24:33,915] [pool-1-thread-1] Initializing /data/geert/good example1.1sc: [testng] [2024-09-19 14:24:36,757] [pool-1-thread-7] Initializing /data/adrian/test_img.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 34 seconds Finished: SUCCESS