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Started by upstream project "BIOFORMATS-test-repo" build number 243 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins15747502086084609361.sh + '[' perkinelmer-operetta = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_38207_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] 14:12:16,060 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 14:12:16,063 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 14:12:16,063 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 14:12:16,064 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 14:12:16,064 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 14:12:16,065 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 14:12:16,065 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 14:12:16,065 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 14:12:16,066 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 14:12:16,067 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 14:12:16,067 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 14:12:16,067 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 14:12:16,260 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 14:12:16,260 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 14:12:16,294 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 14:12:16,294 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 14:12:16,300 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 14:12:16,301 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 14:12:16,301 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 14:12:16,301 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 14:12:16,301 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 14:12:16,302 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 14:12:16,302 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 236 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-02 14:12:16,313] [main] java.version = 11.0.16 [testng] 14:12:16,317 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 14:12:16,317 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:12:16,364 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-02_14-12-16.log] [testng] 14:12:16,366 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-11-02 14:12:16,369] [main] testng.directory = /data [testng] [2024-11-02 14:12:16,369] [main] testng.configDirectory = /config [testng] [2024-11-02 14:12:16,381] [main] testng.multiplier = 1.0 [testng] [2024-11-02 14:12:16,382] [main] testng.in-memory = false [testng] [2024-11-02 14:12:16,382] [main] testng.allow-missing = false [testng] [2024-11-02 14:12:16,382] [main] user.language = en [testng] [2024-11-02 14:12:16,382] [main] user.country = ${user.country} [testng] [2024-11-02 14:12:16,382] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-02 14:19:55,173] [main] ---------------------------------------- [testng] [2024-11-02 14:19:55,173] [main] Total files: 14681 [testng] [2024-11-02 14:19:55,173] [main] Scan time: 458.79 s (31 ms/file) [testng] [2024-11-02 14:19:55,174] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-02 14:28:09,762] [pool-1-thread-1] Initializing /data/public/omer/006P_M3/006P_M3_overview_fields.png: [testng] 14:28:09,763 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 14:28:09,763 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:28:09,765 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-02_14-28-09.log] [testng] 14:28:09,765 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1abd225e - End of configuration. [testng] [2024-11-02 14:28:09,807] [pool-1-thread-12] Initializing /data/public/idr0034/HipSci Experiment 10 Plate 1__2014-08-21T17_57_35-Measurement1/Images/Index.idx.xml: [testng] 14:28:09,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 14:28:09,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:28:09,808 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-02_14-28-09.log] [testng] 14:28:09,808 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a372756 - End of configuration. [testng] [2024-11-02 14:28:24,238] [pool-1-thread-11] Initializing /data/samples/no-first-series/Index.idx.xml: [testng] 14:28:24,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 14:28:24,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:28:24,240 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-02_14-28-24.log] [testng] 14:28:24,240 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1993727d - End of configuration. [testng] [2024-11-02 14:28:24,759] [pool-1-thread-10] Initializing /data/public/zenodo-7841360/Hoechst__2023-03-07T10_17_54-Measurement 2/Images/Index.idx.xml: [testng] 14:28:24,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 14:28:24,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:28:24,760 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-02_14-28-24.log] [testng] 14:28:24,760 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d5dec51 - End of configuration. [testng] [2024-11-02 14:28:25,192] [pool-1-thread-9] Initializing /data/public/omer/006P_M3/006P_M3_overview.png: [testng] 14:28:25,193 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 14:28:25,193 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:28:25,194 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-02_14-28-25.log] [testng] 14:28:25,195 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6639b482 - End of configuration. [testng] [2024-11-02 14:28:25,233] [pool-1-thread-8] Initializing /data/stephen/P004-CC Edu-pHH3__2009-02-03T17_36_29-Measurement1/Images/Index.idx.xml: [testng] 14:28:25,233 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 14:28:25,233 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:28:25,234 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-02_14-28-25.log] [testng] 14:28:25,234 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6560ad1b - End of configuration. [testng] [2024-11-02 14:28:26,169] [pool-1-thread-7] Initializing /data/samples/32-bit-file/Index.idx.xml: [testng] 14:28:26,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 14:28:26,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:28:26,170 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-02_14-28-26.log] [testng] 14:28:26,170 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e9ef95d - End of configuration. [testng] [2024-11-02 14:28:26,759] [pool-1-thread-6] Initializing /data/pki/Export/HRMNY-13786__2021-11-23T13_44_30-Measurement 3/Images/Index.xml: [testng] 14:28:26,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 14:28:26,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:28:26,760 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-02_14-28-26.log] [testng] 14:28:26,761 |-INFO in ch.qos.logback.core.sift.SiftProcessor@361b85d - End of configuration. [testng] [2024-11-02 14:28:27,677] [pool-1-thread-5] Initializing /data/samples/new-phenix/original/Hiplex_run1_cycle1_MsPos/Index.idx.xml: [testng] 14:28:27,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 14:28:27,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:28:27,678 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-02_14-28-27.log] [testng] 14:28:27,678 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3eef234b - End of configuration. [testng] [2024-11-02 14:28:29,171] [pool-1-thread-4] Initializing /data/qa-17826/JLM-20170801-Operetta/Index.idx.xml: [testng] 14:28:29,171 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 14:28:29,171 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:28:29,172 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-02_14-28-29.log] [testng] 14:28:29,172 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3279d908 - End of configuration. [testng] [2024-11-02 14:28:29,926] [pool-1-thread-3] Initializing /data/samples/extra-directories/Index.idx.xml: [testng] 14:28:29,927 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 14:28:29,927 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:28:29,927 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-02_14-28-29.log] [testng] 14:28:29,928 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7efeabde - End of configuration. [testng] [2024-11-02 14:28:30,987] [pool-1-thread-2] Initializing /data/public/omer/006P_M3/006P__2017-08-19T12_42_59-Measurement 3/Images/Index.idx.xml: [testng] 14:28:30,987 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 14:28:30,987 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:28:30,988 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-02_14-28-30.log] [testng] 14:28:30,988 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c1c149c - End of configuration. [testng] [2024-11-02 14:28:36,537] [pool-1-thread-9] Initializing /data/pki/DataSet/dec61bf8-5ca8-415a-8639-b75bf59ca47c/images/index.xml: [testng] [2024-11-02 14:28:37,865] [pool-1-thread-1] Initializing /data/samples/new-phenix/artificial-v6/Hiplex_run1_cycle1_MsPos/Index.idx.xml: [testng] [2024-11-02 14:28:45,683] [pool-1-thread-10] Initializing /data/hms/ryang_skbr3_p1__2012-07-10T15_24_30-Measurement1/Images/Index.idx.xml: [testng] [2024-11-02 14:29:17,322] [pool-1-thread-11] Initializing /data/samples/smaller-xy/Index.idx.xml: [testng] [2024-11-02 14:29:20,690] [pool-1-thread-4] Initializing /data/stephen/Plate 1(2)__2011-09-29T23_50_20-Measurement1/Images/Index.idx.xml: [testng] 16:04:16,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 16:04:16,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:04:16,964 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-02_16-04-16.log] [testng] 16:04:16,964 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b345785 - End of configuration. [testng] 16:16:27,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 16:16:27,003 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:16:27,006 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-02_16-16-27.log] [testng] 16:16:27,007 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71871601 - End of configuration. [testng] 16:16:32,171 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 16:16:32,172 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:16:32,173 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-02_16-16-32.log] [testng] 16:16:32,174 |-INFO in ch.qos.logback.core.sift.SiftProcessor@70d9e606 - End of configuration. [testng] 16:16:48,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 16:16:48,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:16:48,976 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-02_16-16-48.log] [testng] 16:16:48,976 |-INFO in ch.qos.logback.core.sift.SiftProcessor@317e7b4a - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 901, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 124 minutes 36 seconds Finished: SUCCESS