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Started by upstream project "BIOFORMATS-test-repo" build number 212 originally caused by: Started by upstream project "Trigger" build number 238 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/jenkins7817821606396902539.sh + '[' perkinelmer-operetta = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_33639_merge_ci -v /uod/idr/repos/curated/perkinelmer-operetta:/data -v /uod/idr-scratch/merge-ci/curated/perkinelmer-operetta:/config snoopycrimecop/bioformats:merge_ci -Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR 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] 01:36:48,526 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:36:48,528 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 01:36:48,528 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:36:48,529 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:36:48,529 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:36:48,529 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:36:48,530 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:36:48,530 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:36:48,530 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:36:48,530 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:36:48,531 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:36:48,531 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:36:48,819 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:36:48,819 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:36:48,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:36:48,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:36:48,888 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:36:48,888 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:36:48,888 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:36:48,889 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:36:48,889 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 01:36:48,890 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 01:36:48,890 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 360 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-07 01:36:48,904] [main] java.version = 1.8.0_342 [testng] 01:36:48,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:36:48,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:36:48,972 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-07_01-36-48.log] [testng] 01:36:48,975 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-10-07 01:36:48,978] [main] testng.directory = /data [testng] [2024-10-07 01:36:48,979] [main] testng.configDirectory = /config [testng] [2024-10-07 01:36:48,999] [main] testng.multiplier = 1.0 [testng] [2024-10-07 01:36:48,999] [main] testng.in-memory = false [testng] [2024-10-07 01:36:48,999] [main] testng.allow-missing = false [testng] [2024-10-07 01:36:48,999] [main] user.language = fr [testng] [2024-10-07 01:36:49,000] [main] user.country = FR [testng] [2024-10-07 01:36:49,000] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-07 01:40:14,764] [main] ---------------------------------------- [testng] [2024-10-07 01:40:14,764] [main] Total files: 14663 [testng] [2024-10-07 01:40:14,765] [main] Scan time: 205.764 s (14 ms/file) [testng] [2024-10-07 01:40:14,765] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 16 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-07 01:41:49,203] [pool-1-thread-1] Initializing /data/public/zenodo-7841360/Hoechst__2023-03-07T10_17_54-Measurement 2/Images/Index.idx.xml: [testng] 01:41:49,204 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:41:49,204 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:49,205 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-07_01-41-49.log] [testng] 01:41:49,205 |-INFO in ch.qos.logback.core.sift.SiftProcessor@701c8244 - End of configuration. [testng] [2024-10-07 01:41:49,259] [pool-1-thread-12] Initializing /data/public/omer/006P_M3/006P_M3_overview.png: [testng] 01:41:49,259 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:41:49,259 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:49,260 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-07_01-41-49.log] [testng] 01:41:49,261 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d833547 - End of configuration. [testng] [2024-10-07 01:41:49,268] [pool-1-thread-11] Initializing /data/samples/32-bit-file/Index.idx.xml: [testng] 01:41:49,268 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:41:49,268 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:49,269 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-07_01-41-49.log] [testng] 01:41:49,269 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d8bb4df - End of configuration. [testng] [2024-10-07 01:41:49,343] [pool-1-thread-10] Initializing /data/stephen/Plate 1(2)__2011-09-29T23_50_20-Measurement1/Images/Index.idx.xml: [testng] 01:41:49,343 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:41:49,343 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:49,344 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-07_01-41-49.log] [testng] 01:41:49,345 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24097f9e - End of configuration. [testng] [2024-10-07 01:41:49,437] [pool-1-thread-9] Initializing /data/pki/Export/HRMNY-13786__2021-11-23T13_44_30-Measurement 3/Images/Index.xml: [testng] 01:41:49,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:41:49,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:49,438 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-07_01-41-49.log] [testng] 01:41:49,438 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3fef2f04 - End of configuration. [testng] [2024-10-07 01:41:49,566] [pool-1-thread-8] Initializing /data/public/omer/006P_M3/006P__2017-08-19T12_42_59-Measurement 3/Images/Index.idx.xml: [testng] 01:41:49,566 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:41:49,566 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:49,567 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-07_01-41-49.log] [testng] 01:41:49,567 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b1419a3 - End of configuration. [testng] [2024-10-07 01:41:50,048] [pool-1-thread-7] Initializing /data/pki/DataSet/dec61bf8-5ca8-415a-8639-b75bf59ca47c/images/index.xml: [testng] 01:41:50,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:41:50,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:50,050 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-07_01-41-50.log] [testng] 01:41:50,050 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3351e1dc - End of configuration. [testng] [2024-10-07 01:41:50,198] [pool-1-thread-6] Initializing /data/samples/no-first-series/Index.idx.xml: [testng] 01:41:50,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:41:50,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:50,199 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-07_01-41-50.log] [testng] 01:41:50,199 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6cb42a60 - End of configuration. [testng] [2024-10-07 01:41:50,276] [pool-1-thread-5] Initializing /data/samples/new-phenix/artificial-v6/Hiplex_run1_cycle1_MsPos/Index.idx.xml: [testng] 01:41:50,276 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:41:50,276 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:50,276 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-07_01-41-50.log] [testng] 01:41:50,277 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d90038a - End of configuration. [testng] [2024-10-07 01:41:50,692] [pool-1-thread-4] Initializing /data/public/omer/006P_M3/006P_M3_overview_fields.png: [testng] 01:41:50,692 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:41:50,692 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:50,692 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-07_01-41-50.log] [testng] 01:41:50,693 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7479e8d8 - End of configuration. [testng] [2024-10-07 01:41:50,703] [pool-1-thread-3] Initializing /data/qa-17826/JLM-20170801-Operetta/Index.idx.xml: [testng] 01:41:50,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:41:50,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:50,704 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-07_01-41-50.log] [testng] 01:41:50,704 |-INFO in ch.qos.logback.core.sift.SiftProcessor@385fc257 - End of configuration. [testng] [2024-10-07 01:41:50,767] [pool-1-thread-2] Initializing /data/hms/ryang_skbr3_p1__2012-07-10T15_24_30-Measurement1/Images/Index.idx.xml: [testng] 01:41:50,767 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:41:50,768 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:50,768 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-07_01-41-50.log] [testng] 01:41:50,768 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c4d0cc2 - End of configuration. [testng] [2024-10-07 01:41:52,275] [pool-1-thread-12] Initializing /data/samples/new-phenix/original/Hiplex_run1_cycle1_MsPos/Index.idx.xml: [testng] [2024-10-07 01:41:53,013] [pool-1-thread-4] Initializing /data/public/idr0034/HipSci Experiment 10 Plate 1__2014-08-21T17_57_35-Measurement1/Images/Index.idx.xml: [testng] [2024-10-07 01:41:56,859] [pool-1-thread-1] Initializing /data/stephen/P004-CC Edu-pHH3__2009-02-03T17_36_29-Measurement1/Images/Index.idx.xml: [testng] [2024-10-07 01:42:09,433] [pool-1-thread-2] Initializing /data/samples/smaller-xy/Index.idx.xml: [testng] 02:46:25,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:46:25,042 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:25,043 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-07_02-46-25.log] [testng] 02:46:25,043 |-INFO in ch.qos.logback.core.sift.SiftProcessor@db005b - End of configuration. [testng] 02:46:32,064 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:46:32,064 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:46:32,066 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-07_02-46-32.log] [testng] 02:46:32,067 |-INFO in ch.qos.logback.core.sift.SiftProcessor@123d803a - End of configuration. [testng] 02:47:02,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:47:02,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:47:02,802 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-07_02-47-02.log] [testng] 02:47:02,803 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6619b627 - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 848, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 70 minutes 17 seconds Finished: SUCCESS