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Started by upstream project "BIOFORMATS-test-repo" build number 209 originally caused by: Started by upstream project "Trigger" build number 235 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins10043384241443638038.sh + '[' scanr = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_33234_merge_ci -v /uod/idr/repos/curated/scanr:/data -v /uod/idr-scratch/merge-ci/curated/scanr:/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 test-automated: [testng] File leak detector installed [testng] 03:20:26,711 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:20:26,712 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 03:20:26,713 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:20:26,714 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:20:26,714 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:20:26,714 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:20:26,714 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 03:20:26,714 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:20:26,715 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:20:26,715 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:20:26,715 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:20:26,715 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:20:27,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:20:27,032 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:20:27,078 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:20:27,078 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:20:27,092 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:20:27,092 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:20:27,092 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:20:27,093 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:20:27,093 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 03:20:27,094 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 03:20:27,095 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 380 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-04 03:20:27,111] [main] java.version = 1.8.0_342 [testng] 03:20:27,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:20:27,117 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:20:27,185 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-04_03-20-27.log] [testng] 03:20:27,187 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-10-04 03:20:27,189] [main] testng.directory = /data [testng] [2024-10-04 03:20:27,189] [main] testng.configDirectory = /config [testng] [2024-10-04 03:20:27,202] [main] testng.multiplier = 1.0 [testng] [2024-10-04 03:20:27,203] [main] testng.in-memory = false [testng] [2024-10-04 03:20:27,203] [main] testng.allow-missing = false [testng] [2024-10-04 03:20:27,203] [main] user.language = en [testng] [2024-10-04 03:20:27,203] [main] user.country = ${user.country} [testng] [2024-10-04 03:20:27,203] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-04 03:25:18,383] [main] ---------------------------------------- [testng] [2024-10-04 03:25:18,384] [main] Total files: 2169 [testng] [2024-10-04 03:25:18,384] [main] Scan time: 291.18 s (134 ms/file) [testng] [2024-10-04 03:25:18,384] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-04 03:43:26,224] [pool-1-thread-1] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: [testng] 03:43:26,225 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:43:26,225 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:43:26,227 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-04_03-43-26.log] [testng] 03:43:26,227 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26f41844 - End of configuration. [testng] [2024-10-04 03:43:33,411] [pool-1-thread-12] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: [testng] 03:43:33,411 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:43:33,411 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:43:33,412 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-04_03-43-33.log] [testng] 03:43:33,413 |-INFO in ch.qos.logback.core.sift.SiftProcessor@778d0fc6 - End of configuration. [testng] [2024-10-04 03:45:17,234] [pool-1-thread-11] Initializing /data/juergen/Experiment/experiment_descriptor.xml: [testng] 03:45:17,234 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:45:17,234 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:17,235 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-04_03-45-17.log] [testng] 03:45:17,236 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65c752cf - End of configuration. [testng] [2024-10-04 03:45:17,798] [pool-1-thread-10] Initializing /data/ruben/plate_002/experiment_descriptor.xml: [testng] 03:45:17,798 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:45:17,798 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:17,798 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-04_03-45-17.log] [testng] 03:45:17,799 |-INFO in ch.qos.logback.core.sift.SiftProcessor@97c582e - End of configuration. [testng] [2024-10-04 03:45:19,353] [pool-1-thread-9] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: [testng] 03:45:19,353 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:45:19,354 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:19,354 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-04_03-45-19.log] [testng] 03:45:19,355 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15eaeb6 - End of configuration. [testng] [2024-10-04 03:46:57,699] [pool-1-thread-8] Initializing /data/nadine/experiment_descriptor.xml: [testng] 03:46:57,700 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:46:57,700 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:46:57,702 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-04_03-46-57.log] [testng] 03:46:57,702 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a788226 - End of configuration. [testng] [2024-10-04 03:46:58,513] [pool-1-thread-7] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: [testng] 03:46:58,514 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:46:58,514 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:46:58,514 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-04_03-46-58.log] [testng] 03:46:58,515 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e34d15b - End of configuration. [testng] [2024-10-04 03:47:17,909] [pool-1-thread-6] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: [testng] 03:47:17,909 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:47:17,909 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:47:17,910 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-04_03-47-17.log] [testng] 03:47:17,910 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33dee56c - End of configuration. [testng] [2024-10-04 03:48:36,306] [pool-1-thread-5] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: [testng] 03:48:36,307 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:48:36,307 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:48:36,308 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-04_03-48-36.log] [testng] 03:48:36,309 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7dfed5dd - End of configuration. [testng] [2024-10-04 03:48:53,009] [pool-1-thread-4] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: [testng] 03:48:53,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:48:53,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:48:53,009 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-04_03-48-53.log] [testng] 03:48:53,010 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46334fca - End of configuration. [testng] [2024-10-04 03:49:32,161] [pool-1-thread-3] Initializing /data/christian/example/experiment_descriptor.xml: [testng] 03:49:32,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:49:32,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:49:32,162 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-04_03-49-32.log] [testng] 03:49:32,162 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ee3a40f - End of configuration. [testng] [2024-10-04 03:49:32,577] [pool-1-thread-2] Initializing /data/gideon/experiment_descriptor.xml: [testng] 03:49:32,577 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:49:32,577 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:49:32,578 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-04_03-49-32.log] [testng] 03:49:32,578 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c31d701 - End of configuration. [testng] [2024-10-04 03:49:58,716] [pool-1-thread-3] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: [testng] [2024-10-04 03:51:49,322] [pool-1-thread-11] Initializing /data/embl/Maik_001/experiment_descriptor.xml: [testng] [2024-10-04 03:51:58,676] [pool-1-thread-8] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: [testng] [2024-10-04 03:53:21,405] [pool-1-thread-10] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: [testng] [2024-10-04 03:57:29,827] [pool-1-thread-11] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 901, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 82 minutes 1 second Finished: SUCCESS