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Started by upstream project "BIOFORMATS-test-repo" build number 279 originally caused by: Started by upstream project "Trigger" build number 299 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/jenkins8885759564307071726.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_44077_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] 03:12:24,791 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:12:24,792 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 03:12:24,792 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:12:24,793 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:12:24,794 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:12:24,794 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:12:24,794 |-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] 03:12:24,794 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:12:24,795 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:12:24,795 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:12:24,796 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:12:24,796 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:12:24,967 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:12:24,967 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:12:24,989 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:12:24,989 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:12:24,995 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:12:24,995 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:12:24,995 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:12:24,996 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:12:24,996 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 03:12:24,997 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 03:12:24,997 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 202 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-04 03:12:25,006] [main] java.version = 17.0.2 [testng] 03:12:25,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:12:25,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:12:25,049 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-04_03-12-25.log] [testng] 03:12:25,051 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-12-04 03:12:25,053] [main] testng.directory = /data [testng] [2024-12-04 03:12:25,053] [main] testng.configDirectory = /config [testng] [2024-12-04 03:12:25,062] [main] testng.multiplier = 1.0 [testng] [2024-12-04 03:12:25,062] [main] testng.in-memory = false [testng] [2024-12-04 03:12:25,062] [main] testng.allow-missing = false [testng] [2024-12-04 03:12:25,062] [main] user.language = en [testng] [2024-12-04 03:12:25,063] [main] user.country = ${user.country} [testng] [2024-12-04 03:12:25,063] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-04 03:12:27,147] [main] ---------------------------------------- [testng] [2024-12-04 03:12:27,148] [main] Total files: 32 [testng] [2024-12-04 03:12:27,148] [main] Scan time: 2.084 s (65 ms/file) [testng] [2024-12-04 03:12:27,148] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-04 03:12:40,254] [pool-1-thread-1] Initializing /data/samples/Criterion.1sc: [testng] 03:12:40,255 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:12:40,255 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:12:40,256 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-04_03-12-40.log] [testng] 03:12:40,256 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12019f12 - End of configuration. [testng] [2024-12-04 03:12:40,511] [pool-1-thread-12] Initializing /data/qa-29459/bad.jpg: [testng] 03:12:40,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:12:40,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:12:40,512 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-04_03-12-40.log] [testng] 03:12:40,512 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68324a79 - End of configuration. [testng] [2024-12-04 03:12:40,605] [pool-1-thread-11] Initializing /data/david/Opened in imageJ.tiff: [testng] 03:12:40,605 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:12:40,605 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:12:40,606 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-04_03-12-40.log] [testng] 03:12:40,607 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ad57120 - End of configuration. [testng] [2024-12-04 03:12:41,408] [pool-1-thread-10] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] 03:12:41,409 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:12:41,409 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:12:41,410 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-04_03-12-41.log] [testng] 03:12:41,410 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8f2e4b3 - End of configuration. [testng] [2024-12-04 03:12:42,246] [pool-1-thread-9] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [testng] 03:12:42,246 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:12:42,246 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:12:42,247 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-04_03-12-42.log] [testng] 03:12:42,247 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40302b1 - End of configuration. [testng] [2024-12-04 03:12:43,264] [pool-1-thread-8] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] 03:12:43,265 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:12:43,265 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:12:43,266 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-04_03-12-43.log] [testng] 03:12:43,266 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ddee535 - End of configuration. [testng] [2024-12-04 03:12:43,512] [pool-1-thread-7] Initializing /data/samples/imagesEight.1sc: [testng] 03:12:43,512 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:12:43,512 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:12:43,513 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-04_03-12-43.log] [testng] 03:12:43,513 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60a01aef - End of configuration. [testng] [2024-12-04 03:12:43,766] [pool-1-thread-6] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] 03:12:43,766 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:12:43,766 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:12:43,767 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-04_03-12-43.log] [testng] 03:12:43,767 |-INFO in ch.qos.logback.core.sift.SiftProcessor@656cab21 - End of configuration. [testng] [2024-12-04 03:12:44,678] [pool-1-thread-5] Initializing /data/keith/test2.1sc: [testng] 03:12:44,678 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:12:44,679 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:12:44,679 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-04_03-12-44.log] [testng] 03:12:44,680 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1961b56a - End of configuration. [testng] [2024-12-04 03:12:44,964] [pool-1-thread-4] Initializing /data/david/Original Biorad Gel format file.1sc: [testng] 03:12:44,964 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:12:44,964 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:12:44,965 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-04_03-12-44.log] [testng] 03:12:44,966 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72a76891 - End of configuration. [testng] [2024-12-04 03:12:45,242] [pool-1-thread-3] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] 03:12:45,242 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:12:45,242 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:12:45,243 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-04_03-12-45.log] [testng] 03:12:45,244 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ee4d402 - End of configuration. [testng] [2024-12-04 03:12:46,221] [pool-1-thread-2] Initializing /data/geert/bad example1.1sc: [testng] 03:12:46,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:12:46,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:12:46,222 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-04_03-12-46.log] [testng] 03:12:46,222 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1193bec3 - End of configuration. [testng] [2024-12-04 03:12:51,262] [pool-1-thread-12] Initializing /data/qa-29469/good.1sc: [testng] [2024-12-04 03:12:51,841] [pool-1-thread-7] Initializing /data/qa-29469/bad3.1sc: [testng] [2024-12-04 03:12:52,596] [pool-1-thread-5] Initializing /data/qa-29459/bad.1sc: [testng] [2024-12-04 03:12:53,238] [pool-1-thread-1] Initializing /data/keith/pg020410saur3.1sc: [testng] [2024-12-04 03:12:53,797] [pool-1-thread-2] Initializing /data/geert/bad example1.1sc.jpg: [testng] [2024-12-04 03:12:53,947] [pool-1-thread-8] Initializing /data/adrian/test_img.1sc: [testng] [2024-12-04 03:12:54,355] [pool-1-thread-4] Initializing /data/sylvain/2009-10-26 14hr 59min: [testng] [2024-12-04 03:12:58,244] [pool-1-thread-12] Initializing /data/keith/PF020426MRSA v2.1sc: [testng] [2024-12-04 03:12:59,008] [pool-1-thread-7] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] [2024-12-04 03:13:00,228] [pool-1-thread-1] Initializing /data/keith/PF020328saur v3.1sc: [testng] [2024-12-04 03:13:01,050] [pool-1-thread-5] Initializing /data/keith/test.1sc: [testng] [2024-12-04 03:13:01,661] [pool-1-thread-4] Initializing /data/qa-16880/c-src v7.1sc: [testng] [2024-12-04 03:13:02,184] [pool-1-thread-3] Initializing /data/geert/good example1.1sc.jpg: [testng] [2024-12-04 03:13:02,374] [pool-1-thread-8] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] [2024-12-04 03:13:02,928] [pool-1-thread-11] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] [2024-12-04 03:13:03,463] [pool-1-thread-6] Initializing /data/geert/good example1.1sc: [testng] [2024-12-04 03:13:03,950] [pool-1-thread-10] Initializing /data/geert/bad example1.jpg: [testng] [2024-12-04 03:13:04,154] [pool-1-thread-9] Initializing /data/qa-29469/bad2.1sc: [testng] [2024-12-04 03:13:04,666] [pool-1-thread-2] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] [2024-12-04 03:13:09,429] [pool-1-thread-3] Initializing /data/sylvain/2009-10-23 12hr 18min.tif: [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 2 seconds Finished: SUCCESS