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Started by upstream project "BIOFORMATS-test-repo" build number 384 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins16333917562000227061.sh + '[' mias = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_60842_merge_ci -v /uod/idr/repos/curated/mias:/data -v /uod/idr-scratch/merge-ci/curated/mias:/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] 21:44:18,573 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 21:44:18,574 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service. [testng] 21:44:18,574 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 21:44:18,575 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 21:44:18,576 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 21:44:18,576 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 21:44:18,576 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 21:44:18,576 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 21:44:18,577 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 21:44:18,577 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 21:44:18,577 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 21:44:18,578 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 21:44:18,724 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 21:44:18,724 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 21:44:18,744 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 21:44:18,744 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 21:44:18,749 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 21:44:18,749 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 21:44:18,749 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 21:44:18,749 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 21:44:18,749 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration. [testng] 21:44:18,750 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point [testng] 21:44:18,750 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 173 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-19 21:44:18,758] [main] java.version = 17.0.2 [testng] 21:44:18,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 21:44:18,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 21:44:18,798 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-19_21-44-18.log] [testng] 21:44:18,799 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration. [testng] [2025-03-19 21:44:18,801] [main] testng.directory = /data [testng] [2025-03-19 21:44:18,801] [main] testng.configDirectory = /config [testng] [2025-03-19 21:44:18,809] [main] testng.multiplier = 1.0 [testng] [2025-03-19 21:44:18,809] [main] testng.in-memory = false [testng] [2025-03-19 21:44:18,810] [main] testng.allow-missing = false [testng] [2025-03-19 21:44:18,810] [main] user.language = en [testng] [2025-03-19 21:44:18,810] [main] user.country = ${user.country} [testng] [2025-03-19 21:44:18,810] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-19 21:44:52,983] [main] ---------------------------------------- [testng] [2025-03-19 21:44:52,983] [main] Total files: 12 [testng] [2025-03-19 21:44:52,983] [main] Scan time: 34.173 s (2847 ms/file) [testng] [2025-03-19 21:44:52,983] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 7 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-19 21:48:59,761] [pool-1-thread-1] Initializing /data/frans/MIAS 3D set 3 july 13 2009/001/0074/1/001_001_000_000.tif: [testng] 21:48:59,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 21:48:59,762 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 21:48:59,763 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-19_21-48-59.log] [testng] 21:48:59,763 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d189465 - End of configuration. [testng] [2025-03-19 21:49:02,859] [pool-1-thread-7] Initializing /data/frans/MIAS 3 D set 2 july 13 2009/001/0018/1/001_001_000_000.tif: [testng] 21:49:02,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 21:49:02,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 21:49:02,860 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-19_21-49-02.log] [testng] 21:49:02,860 |-INFO in ch.qos.logback.core.sift.SiftProcessor@307e1263 - End of configuration. [testng] [2025-03-19 21:49:06,055] [pool-1-thread-6] Initializing /data/frans/siRNA_PRIM1_03102008/001-365700055641/Well0001/mode1_z000_t000_im1_1.tif: [testng] 21:49:06,055 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 21:49:06,055 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 21:49:06,056 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-19_21-49-06.log] [testng] 21:49:06,056 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78bee4bb - End of configuration. [testng] [2025-03-19 21:49:10,181] [pool-1-thread-5] Initializing /data/frans/NEO-Exp13072008-long-protokol/004-365700055549/Well0001/mode1_z000_t000_im1_1.tif: [testng] 21:49:10,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 21:49:10,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 21:49:10,182 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-19_21-49-10.log] [testng] 21:49:10,182 |-INFO in ch.qos.logback.core.sift.SiftProcessor@cc9158d - End of configuration. [testng] [2025-03-19 21:49:16,514] [pool-1-thread-4] Initializing /data/frans/One MNU Plate/001/Well0014/mode1_z000_t000_im1_1.tif: [testng] 21:49:16,514 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 21:49:16,514 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 21:49:16,515 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-19_21-49-16.log] [testng] 21:49:16,515 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33d3b67f - End of configuration. [testng] [2025-03-19 21:49:20,328] [pool-1-thread-3] Initializing /data/frans/NEO-Exp13072008-long-protokol/005-365700055480/Well0001/mode1_z000_t000_im1_1.tif: [testng] 21:49:20,328 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 21:49:20,329 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 21:49:20,329 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-19_21-49-20.log] [testng] 21:49:20,330 |-INFO in ch.qos.logback.core.sift.SiftProcessor@771c5da1 - End of configuration. [testng] [2025-03-19 21:49:27,465] [pool-1-thread-2] Initializing /data/frans/NEO-Exp13072008-long-protokol/001-365700055641/Well0001/mode1_z000_t000_im1_1.tif: [testng] 21:49:27,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 21:49:27,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 21:49:27,466 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-19_21-49-27.log] [testng] 21:49:27,467 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72f5b3af - End of configuration. [testng] 23:31:02,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 23:31:02,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 23:31:02,938 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-19_23-31-02.log] [testng] 23:31:02,938 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f7b92a5 - End of configuration. time="2025-03-20T01:01:31Z" level=error msg="error waiting for container: unexpected EOF" Build step 'Execute shell' marked build as failure Finished: FAILURE