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Started by upstream project "BIOFORMATS-test-repo" build number 9 originally caused by: Started by upstream project "Trigger" build number 12 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/jenkins6673932828604313742.sh + '[' perkinelmer-operetta = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_1321_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 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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 00:30:48,103 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:30:48,105 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 00:30:48,105 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:30:48,107 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:30:48,107 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:30:48,107 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:30:48,108 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:30:48,108 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:30:48,108 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:30:48,109 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:30:48,109 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:30:48,109 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:30:48,310 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:30:48,310 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:30:48,334 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:30:48,335 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:30:48,341 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:30:48,341 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:30:48,341 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:30:48,341 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:30:48,342 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 00:30:48,342 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 00:30:48,342 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 234 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-23 00:30:48,356] [main] java.version = 11.0.16 [testng] 00:30:48,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:30:48,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:48,406 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-23_00-30-48.log] [testng] 00:30:48,408 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-03-23 00:30:48,410] [main] testng.directory = /data [testng] [2024-03-23 00:30:48,410] [main] testng.configDirectory = /config [testng] [2024-03-23 00:30:48,421] [main] testng.multiplier = 1.0 [testng] [2024-03-23 00:30:48,422] [main] testng.in-memory = false [testng] [2024-03-23 00:30:48,422] [main] testng.allow-missing = false [testng] [2024-03-23 00:30:48,422] [main] user.language = en [testng] [2024-03-23 00:30:48,422] [main] user.country = ${user.country} [testng] [2024-03-23 00:30:48,422] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-23 00:33:40,823] [main] ---------------------------------------- [testng] [2024-03-23 00:33:40,824] [main] Total files: 14659 [testng] [2024-03-23 00:33:40,824] [main] Scan time: 172.4 s (11 ms/file) [testng] [2024-03-23 00:33:40,824] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-23 00:34:42,457] [pool-1-thread-1] Initializing /data/pki/Export/HRMNY-13786__2021-11-23T13_44_30-Measurement 3/Images/Index.xml: [testng] 00:34:42,458 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:34:42,458 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:42,459 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-23_00-34-42.log] [testng] 00:34:42,460 |-INFO in ch.qos.logback.core.sift.SiftProcessor@690bf460 - End of configuration. [testng] [2024-03-23 00:34:42,568] [pool-1-thread-12] Initializing /data/public/omer/006P_M3/006P_M3_overview_fields.png: [testng] 00:34:42,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:34:42,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:42,569 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-23_00-34-42.log] [testng] 00:34:42,570 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65165552 - End of configuration. [testng] [2024-03-23 00:34:42,579] [pool-1-thread-11] Initializing /data/samples/new-phenix/original/Hiplex_run1_cycle1_MsPos/Index.idx.xml: [testng] 00:34:42,579 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:34:42,579 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:42,580 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-23_00-34-42.log] [testng] 00:34:42,580 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7202520a - End of configuration. [testng] [2024-03-23 00:34:43,248] [pool-1-thread-10] Initializing /data/public/omer/006P_M3/006P_M3_overview.png: [testng] 00:34:43,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:34:43,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:43,250 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-23_00-34-43.log] [testng] 00:34:43,250 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e0129a1 - End of configuration. [testng] [2024-03-23 00:34:43,260] [pool-1-thread-9] Initializing /data/public/idr0034/HipSci Experiment 10 Plate 1__2014-08-21T17_57_35-Measurement1/Images/Index.idx.xml: [testng] 00:34:43,260 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:34:43,260 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:43,261 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-23_00-34-43.log] [testng] 00:34:43,262 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ceb6563 - End of configuration. [testng] [2024-03-23 00:34:44,287] [pool-1-thread-8] Initializing /data/samples/no-first-series/Index.idx.xml: [testng] 00:34:44,287 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:34:44,288 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:44,288 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-23_00-34-44.log] [testng] 00:34:44,289 |-INFO in ch.qos.logback.core.sift.SiftProcessor@740ca14a - End of configuration. [testng] [2024-03-23 00:34:44,323] [pool-1-thread-7] Initializing /data/samples/smaller-xy/Index.idx.xml: [testng] 00:34:44,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:34:44,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:44,324 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-23_00-34-44.log] [testng] 00:34:44,324 |-INFO in ch.qos.logback.core.sift.SiftProcessor@182f1328 - End of configuration. [testng] [2024-03-23 00:34:44,359] [pool-1-thread-6] Initializing /data/qa-17826/JLM-20170801-Operetta/Index.idx.xml: [testng] 00:34:44,359 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:34:44,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:44,360 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-23_00-34-44.log] [testng] 00:34:44,361 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7daa9f14 - End of configuration. [testng] [2024-03-23 00:34:44,406] [pool-1-thread-5] Initializing /data/public/omer/006P_M3/006P__2017-08-19T12_42_59-Measurement 3/Images/Index.idx.xml: [testng] 00:34:44,406 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:34:44,406 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:44,407 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-23_00-34-44.log] [testng] 00:34:44,407 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44938eea - End of configuration. [testng] [2024-03-23 00:34:44,673] [pool-1-thread-4] Initializing /data/pki/DataSet/dec61bf8-5ca8-415a-8639-b75bf59ca47c/images/index.xml: [testng] 00:34:44,673 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:34:44,673 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:44,674 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-23_00-34-44.log] [testng] 00:34:44,674 |-INFO in ch.qos.logback.core.sift.SiftProcessor@560a82fe - End of configuration. [testng] [2024-03-23 00:34:44,754] [pool-1-thread-3] Initializing /data/stephen/P004-CC Edu-pHH3__2009-02-03T17_36_29-Measurement1/Images/Index.idx.xml: [testng] 00:34:44,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:34:44,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:44,755 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-23_00-34-44.log] [testng] 00:34:44,755 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9a9f163 - End of configuration. [testng] [2024-03-23 00:34:44,822] [pool-1-thread-2] Initializing /data/samples/32-bit-file/Index.idx.xml: [testng] 00:34:44,822 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:34:44,822 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:44,823 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-23_00-34-44.log] [testng] 00:34:44,823 |-INFO in ch.qos.logback.core.sift.SiftProcessor@360e2a54 - End of configuration. [testng] [2024-03-23 00:34:46,388] [pool-1-thread-10] Initializing /data/hms/ryang_skbr3_p1__2012-07-10T15_24_30-Measurement1/Images/Index.idx.xml: [testng] [2024-03-23 00:34:46,438] [pool-1-thread-12] Initializing /data/samples/new-phenix/artificial-v6/Hiplex_run1_cycle1_MsPos/Index.idx.xml: [testng] [2024-03-23 00:34:56,731] [pool-1-thread-8] Initializing /data/stephen/Plate 1(2)__2011-09-29T23_50_20-Measurement1/Images/Index.idx.xml: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 795, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 41 minutes 11 seconds Finished: SUCCESS