![[Jenkins]](/jenkins/static/7a3257c3/images/svgs/logo.svg){kind=logo}
Started by upstream project "BIOFORMATS-test-repo" build number 361 originally caused by: Started by upstream project "Trigger" build number 387 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins7338079602003666355.sh + '[' perkinelmer-operetta = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_57507_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] 00:37:07,421 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:37:07,422 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - No custom configurators were discovered as a service. [testng] 00:37:07,422 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:37:07,423 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:37:07,424 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:37:07,424 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:37:07,425 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:37:07,425 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:37:07,425 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:37:07,426 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:37:07,426 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:37:07,426 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:37:07,651 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:37:07,651 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:37:07,674 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:37:07,674 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:37:07,679 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:37:07,679 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:37:07,679 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:37:07,680 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:37:07,680 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@65c7a252 - End of configuration. [testng] 00:37:07,681 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@38cee291 - Registering current configuration as safe fallback point [testng] 00:37:07,681 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 256 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-01 00:37:07,693] [main] java.version = 11.0.16 [testng] 00:37:07,697 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:37:07,697 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:37:07,762 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-01_00-37-07.log] [testng] 00:37:07,764 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13d73f29 - End of configuration. [testng] [2025-03-01 00:37:07,767] [main] testng.directory = /data [testng] [2025-03-01 00:37:07,768] [main] testng.configDirectory = /config [testng] [2025-03-01 00:37:07,778] [main] testng.multiplier = 1.0 [testng] [2025-03-01 00:37:07,779] [main] testng.in-memory = false [testng] [2025-03-01 00:37:07,779] [main] testng.allow-missing = false [testng] [2025-03-01 00:37:07,779] [main] user.language = en [testng] [2025-03-01 00:37:07,779] [main] user.country = ${user.country} [testng] [2025-03-01 00:37:07,779] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-01 00:42:23,883] [main] ---------------------------------------- [testng] [2025-03-01 00:42:23,883] [main] Total files: 14681 [testng] [2025-03-01 00:42:23,884] [main] Scan time: 316.103 s (21 ms/file) [testng] [2025-03-01 00:42:23,884] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-01 00:44:53,531] [pool-1-thread-1] Initializing /data/public/omer/006P_M3/006P_M3_overview_fields.png: [testng] 00:44:53,532 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:44:53,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:53,535 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-01_00-44-53.log] [testng] 00:44:53,535 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4774b30 - End of configuration. [testng] [2025-03-01 00:44:53,553] [pool-1-thread-12] Initializing /data/samples/new-phenix/artificial-v6/Hiplex_run1_cycle1_MsPos/Index.idx.xml: [testng] 00:44:53,553 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:44:53,553 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:53,555 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-01_00-44-53.log] [testng] 00:44:53,555 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b534daf - End of configuration. [testng] [2025-03-01 00:44:54,024] [pool-1-thread-11] Initializing /data/public/omer/006P_M3/006P_M3_overview.png: [testng] 00:44:54,024 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:44:54,024 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:54,025 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-01_00-44-54.log] [testng] 00:44:54,025 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2fb6a720 - End of configuration. [testng] [2025-03-01 00:44:54,035] [pool-1-thread-10] Initializing /data/stephen/P004-CC Edu-pHH3__2009-02-03T17_36_29-Measurement1/Images/Index.idx.xml: [testng] 00:44:54,035 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:44:54,035 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:54,036 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-01_00-44-54.log] [testng] 00:44:54,036 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38dbe294 - End of configuration. [testng] [2025-03-01 00:44:54,214] [pool-1-thread-9] Initializing /data/samples/new-phenix/original/Hiplex_run1_cycle1_MsPos/Index.idx.xml: [testng] 00:44:54,214 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:44:54,214 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:54,215 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-01_00-44-54.log] [testng] 00:44:54,216 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a09a1c5 - End of configuration. [testng] [2025-03-01 00:44:54,715] [pool-1-thread-8] Initializing /data/public/idr0034/HipSci Experiment 10 Plate 1__2014-08-21T17_57_35-Measurement1/Images/Index.idx.xml: [testng] 00:44:54,715 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:44:54,715 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:54,716 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-01_00-44-54.log] [testng] 00:44:54,717 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29c2a1ff - End of configuration. [testng] [2025-03-01 00:44:57,737] [pool-1-thread-7] Initializing /data/pki/DataSet/dec61bf8-5ca8-415a-8639-b75bf59ca47c/images/index.xml: [testng] 00:44:57,737 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:44:57,737 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:57,738 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-01_00-44-57.log] [testng] 00:44:57,738 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e02c473 - End of configuration. [testng] [2025-03-01 00:44:57,978] [pool-1-thread-6] Initializing /data/samples/extra-directories/Index.idx.xml: [testng] 00:44:57,979 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:44:57,979 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:57,979 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-01_00-44-57.log] [testng] 00:44:57,980 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65474e8e - End of configuration. [testng] [2025-03-01 00:44:58,125] [pool-1-thread-5] Initializing /data/stephen/Plate 1(2)__2011-09-29T23_50_20-Measurement1/Images/Index.idx.xml: [testng] 00:44:58,126 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:44:58,126 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:58,126 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-01_00-44-58.log] [testng] 00:44:58,127 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2762beb5 - End of configuration. [testng] [2025-03-01 00:44:58,263] [pool-1-thread-4] Initializing /data/samples/smaller-xy/Index.idx.xml: [testng] 00:44:58,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:44:58,264 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:58,264 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-01_00-44-58.log] [testng] 00:44:58,264 |-INFO in ch.qos.logback.core.sift.SiftProcessor@eba3196 - End of configuration. [testng] [2025-03-01 00:44:58,401] [pool-1-thread-3] Initializing /data/hms/ryang_skbr3_p1__2012-07-10T15_24_30-Measurement1/Images/Index.idx.xml: [testng] 00:44:58,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:44:58,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:58,402 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-01_00-44-58.log] [testng] 00:44:58,402 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e8755ba - End of configuration. [testng] [2025-03-01 00:44:58,552] [pool-1-thread-2] Initializing /data/samples/no-first-series/Index.idx.xml: [testng] 00:44:58,552 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:44:58,552 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:58,553 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-01_00-44-58.log] [testng] 00:44:58,553 |-INFO in ch.qos.logback.core.sift.SiftProcessor@409c0961 - End of configuration. [testng] [2025-03-01 00:45:00,869] [pool-1-thread-11] Initializing /data/public/zenodo-7841360/Hoechst__2023-03-07T10_17_54-Measurement 2/Images/Index.idx.xml: [testng] [2025-03-01 00:45:01,033] [pool-1-thread-1] Initializing /data/pki/Export/HRMNY-13786__2021-11-23T13_44_30-Measurement 3/Images/Index.xml: [testng] [2025-03-01 00:45:06,186] [pool-1-thread-11] Initializing /data/samples/32-bit-file/Index.idx.xml: [testng] [2025-03-01 00:45:18,870] [pool-1-thread-3] Initializing /data/qa-17826/JLM-20170801-Operetta/Index.idx.xml: [testng] [2025-03-01 00:45:19,531] [pool-1-thread-2] Initializing /data/public/omer/006P_M3/006P__2017-08-19T12_42_59-Measurement 3/Images/Index.idx.xml: [testng] 02:13:55,739 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:13:55,739 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:55,740 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-01_02-13-55.log] [testng] 02:13:55,741 |-INFO in ch.qos.logback.core.sift.SiftProcessor@475f63b - End of configuration. [testng] 02:22:19,012 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:22:19,012 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:22:19,014 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-01_02-22-19.log] [testng] 02:22:19,014 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b49b1db - End of configuration. [testng] 02:22:22,920 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:22:22,920 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:22:22,923 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-01_02-22-22.log] [testng] 02:22:22,923 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47f88afa - End of configuration. [testng] 02:22:48,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:22:48,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:22:48,771 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-01_02-22-48.log] [testng] 02:22:48,772 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24053dc1 - 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: 105 minutes 44 seconds Finished: SUCCESS