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Started by upstream project "BIOFORMATS-test-repo" build number 284 originally caused by: Started by upstream project "Trigger" build number 303 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/jenkins12664521809774200755.sh + '[' biorad-gel = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_44899_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] 03:48:22,104 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:48:22,105 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 03:48:22,105 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:48:22,106 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:48:22,106 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:48:22,107 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:48:22,107 |-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] 03:48:22,107 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:48:22,107 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:48:22,108 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:48:22,108 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:48:22,109 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:48:22,268 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:48:22,268 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:48:22,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:48:22,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:48:22,297 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:48:22,298 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:48:22,298 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:48:22,298 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:48:22,298 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 03:48:22,299 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 03:48:22,299 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 192 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-08 03:48:22,307] [main] java.version = 17.0.2 [testng] 03:48:22,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:48:22,311 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:48:22,350 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-08_03-48-22.log] [testng] 03:48:22,352 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-12-08 03:48:22,353] [main] testng.directory = /data [testng] [2024-12-08 03:48:22,354] [main] testng.configDirectory = /config [testng] [2024-12-08 03:48:22,362] [main] testng.multiplier = 1.0 [testng] [2024-12-08 03:48:22,363] [main] testng.in-memory = false [testng] [2024-12-08 03:48:22,363] [main] testng.allow-missing = false [testng] [2024-12-08 03:48:22,363] [main] user.language = en [testng] [2024-12-08 03:48:22,363] [main] user.country = ${user.country} [testng] [2024-12-08 03:48:22,363] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-08 03:48:26,542] [main] ---------------------------------------- [testng] [2024-12-08 03:48:26,542] [main] Total files: 32 [testng] [2024-12-08 03:48:26,543] [main] Scan time: 4.179 s (130 ms/file) [testng] [2024-12-08 03:48:26,543] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 32 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-08 03:48:57,485] [pool-1-thread-1] Initializing /data/samples/Criterion.1sc: [testng] 03:48:57,485 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:48:57,486 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:48:57,487 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-08_03-48-57.log] [testng] 03:48:57,487 |-INFO in ch.qos.logback.core.sift.SiftProcessor@638785a8 - End of configuration. [testng] [2024-12-08 03:48:58,003] [pool-1-thread-12] Initializing /data/qa-29459/bad.jpg: [testng] 03:48:58,003 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:48:58,003 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:48:58,004 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-08_03-48-58.log] [testng] 03:48:58,004 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f81a390 - End of configuration. [testng] [2024-12-08 03:48:58,178] [pool-1-thread-11] Initializing /data/david/Opened in imageJ.tiff: [testng] 03:48:58,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:48:58,178 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:48:58,179 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-08_03-48-58.log] [testng] 03:48:58,179 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66a8d654 - End of configuration. [testng] [2024-12-08 03:49:00,324] [pool-1-thread-10] Initializing /data/sylvain/2009-10-26 14hr 59min.tif: [testng] 03:49:00,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:49:00,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:49:00,324 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-08_03-49-00.log] [testng] 03:49:00,325 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c41162e - End of configuration. [testng] [2024-12-08 03:49:03,563] [pool-1-thread-9] Initializing /data/sylvain/2009-10-26 14hr 56min.tif: [testng] 03:49:03,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:49:03,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:49:03,564 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-08_03-49-03.log] [testng] 03:49:03,565 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64338a9a - End of configuration. [testng] [2024-12-08 03:49:05,495] [pool-1-thread-8] Initializing /data/sylvain/2009-10-23 12hr 19min: [testng] 03:49:05,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:49:05,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:49:05,496 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-08_03-49-05.log] [testng] 03:49:05,497 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1dc48a5 - End of configuration. [testng] [2024-12-08 03:49:06,018] [pool-1-thread-7] Initializing /data/samples/imagesEight.1sc: [testng] 03:49:06,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:49:06,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:49:06,019 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-08_03-49-06.log] [testng] 03:49:06,020 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c3c493a - End of configuration. [testng] [2024-12-08 03:49:06,670] [pool-1-thread-6] Initializing /data/sylvain/2009-10-26 14hr 57min.tif: [testng] 03:49:06,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:49:06,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:49:06,671 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-08_03-49-06.log] [testng] 03:49:06,672 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1af6b47a - End of configuration. [testng] [2024-12-08 03:49:08,584] [pool-1-thread-5] Initializing /data/keith/test2.1sc: [testng] 03:49:08,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:49:08,585 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:49:08,585 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-08_03-49-08.log] [testng] 03:49:08,586 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4cccfb05 - End of configuration. [testng] [2024-12-08 03:49:09,068] [pool-1-thread-4] Initializing /data/david/Original Biorad Gel format file.1sc: [testng] 03:49:09,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:49:09,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:49:09,069 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-08_03-49-09.log] [testng] 03:49:09,069 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29aeaf55 - End of configuration. [testng] [2024-12-08 03:49:09,553] [pool-1-thread-3] Initializing /data/david/Converted in Quantity One (Biorad).tiff: [testng] 03:49:09,553 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:49:09,553 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:49:09,554 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-08_03-49-09.log] [testng] 03:49:09,555 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ca02fd7 - End of configuration. [testng] [2024-12-08 03:49:13,248] [pool-1-thread-2] Initializing /data/geert/bad example1.1sc: [testng] 03:49:13,248 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:49:13,248 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:49:13,249 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-08_03-49-13.log] [testng] 03:49:13,249 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5035f461 - End of configuration. [testng] [2024-12-08 03:49:19,073] [pool-1-thread-12] Initializing /data/qa-29469/good.1sc: [testng] [2024-12-08 03:49:19,518] [pool-1-thread-7] Initializing /data/keith/pg020410saur3.1sc: [testng] [2024-12-08 03:49:19,926] [pool-1-thread-5] Initializing /data/geert/bad example1.1sc.jpg: [testng] [2024-12-08 03:49:20,088] [pool-1-thread-4] Initializing /data/adrian/test_img.1sc: [testng] [2024-12-08 03:49:20,653] [pool-1-thread-1] Initializing /data/sylvain/2009-10-26 14hr 59min: [testng] [2024-12-08 03:49:21,620] [pool-1-thread-2] Initializing /data/qa-29459/bad.1sc: [testng] [2024-12-08 03:49:22,089] [pool-1-thread-8] Initializing /data/qa-29469/bad3.1sc: [testng] [2024-12-08 03:49:27,242] [pool-1-thread-7] Initializing /data/keith/PF020426MRSA v2.1sc: [testng] [2024-12-08 03:49:28,040] [pool-1-thread-2] Initializing /data/sylvain/2009-10-26 14hr 56min: [testng] [2024-12-08 03:49:28,669] [pool-1-thread-12] Initializing /data/keith/PF020328saur v3.1sc: [testng] [2024-12-08 03:49:29,206] [pool-1-thread-1] Initializing /data/geert/good example1.1sc.jpg: [testng] [2024-12-08 03:49:29,390] [pool-1-thread-8] Initializing /data/sylvain/2009-10-26 14hr 57min: [testng] [2024-12-08 03:49:29,948] [pool-1-thread-4] Initializing /data/sylvain/2009-10-23 12hr 18min: [testng] [2024-12-08 03:49:30,454] [pool-1-thread-5] Initializing /data/keith/test.1sc: [testng] [2024-12-08 03:49:31,082] [pool-1-thread-6] Initializing /data/qa-16880/c-src v7.1sc: [testng] [2024-12-08 03:49:31,896] [pool-1-thread-3] Initializing /data/sylvain/2009-10-23 12hr 19min.tif: [testng] [2024-12-08 03:49:34,079] [pool-1-thread-10] Initializing /data/geert/good example1.1sc: [testng] [2024-12-08 03:49:35,030] [pool-1-thread-11] Initializing /data/geert/bad example1.jpg: [testng] [2024-12-08 03:49:35,205] [pool-1-thread-9] Initializing /data/qa-29469/bad2.1sc: [testng] [2024-12-08 03:49:38,177] [pool-1-thread-1] 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 34 seconds Finished: SUCCESS