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Started by upstream project "BIOFORMATS-test-repo" build number 399 originally caused by: Started by upstream project "Trigger" build number 485 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@18 [BIOFORMATS-test-folder@18] $ /bin/bash -xe /tmp/jenkins774328727902877837.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_63000_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] 01:41:06,650 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 01:41:06,651 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - No custom configurators were discovered as a service. [testng] 01:41:06,651 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:41:06,652 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:41:06,653 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:41:06,653 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:41:06,653 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:41:06,653 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:41:06,654 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:41:06,654 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:41:06,654 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:41:06,654 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:41:06,865 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:41:06,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:41:06,892 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:41:06,892 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:41:06,900 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:41:06,900 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:41:06,900 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:41:06,901 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:41:06,901 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@63355449 - End of configuration. [testng] 01:41:06,901 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48ae9b55 - Registering current configuration as safe fallback point [testng] 01:41:06,902 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 248 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-05-19 01:41:06,911] [main] java.version = 1.8.0_342 [testng] 01:41:06,914 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:41:06,914 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:41:06,971 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-05-19_01-41-06.log] [testng] 01:41:06,972 |-INFO in ch.qos.logback.core.sift.SiftProcessor@765d7657 - End of configuration. [testng] [2025-05-19 01:41:06,974] [main] testng.directory = /data [testng] [2025-05-19 01:41:06,974] [main] testng.configDirectory = /config [testng] [2025-05-19 01:41:06,986] [main] testng.multiplier = 1.0 [testng] [2025-05-19 01:41:06,986] [main] testng.in-memory = false [testng] [2025-05-19 01:41:06,986] [main] testng.allow-missing = false [testng] [2025-05-19 01:41:06,986] [main] user.language = fr [testng] [2025-05-19 01:41:06,986] [main] user.country = FR [testng] [2025-05-19 01:41:06,986] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2025-05-19 05:00:59,932] [main] ---------------------------------------- [testng] [2025-05-19 05:00:59,932] [main] Total files: 14681 [testng] [2025-05-19 05:00:59,933] [main] Scan time: 11992.946 s (816 ms/file) [testng] [2025-05-19 05:00:59,933] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-05-19 07:21:36,842] [pool-1-thread-1] Initializing /data/public/omer/006P_M3/006P_M3_overview.png: [testng] 07:21:36,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 07:21:36,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:21:36,843 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-05-19_07-21-36.log] [testng] 07:21:36,844 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bdb04a2 - End of configuration. [testng] [2025-05-19 07:21:37,109] [pool-1-thread-12] Initializing /data/samples/new-phenix/artificial-v6/Hiplex_run1_cycle1_MsPos/Index.idx.xml: [testng] 07:21:37,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 07:21:37,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:21:37,111 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-05-19_07-21-37.log] [testng] 07:21:37,111 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34c066cf - End of configuration. [testng] [2025-05-19 07:21:55,733] [pool-1-thread-11] Initializing /data/public/zenodo-7841360/Hoechst__2023-03-07T10_17_54-Measurement 2/Images/Index.idx.xml: [testng] 07:21:55,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 07:21:55,734 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:21:55,734 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-05-19_07-21-55.log] [testng] 07:21:55,735 |-INFO in ch.qos.logback.core.sift.SiftProcessor@bc7f098 - End of configuration. [testng] [2025-05-19 07:22:02,341] [pool-1-thread-10] Initializing /data/stephen/Plate 1(2)__2011-09-29T23_50_20-Measurement1/Images/Index.idx.xml: [testng] 07:22:02,341 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 07:22:02,341 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:22:02,342 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-05-19_07-22-02.log] [testng] 07:22:02,342 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ecfd165 - End of configuration. [testng] [2025-05-19 07:22:14,154] [pool-1-thread-9] Initializing /data/qa-17826/JLM-20170801-Operetta/Index.idx.xml: [testng] 07:22:14,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 07:22:14,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:22:14,155 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-05-19_07-22-14.log] [testng] 07:22:14,155 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5acf4785 - End of configuration. [testng] [2025-05-19 07:22:21,802] [pool-1-thread-8] Initializing /data/samples/new-phenix/original/Hiplex_run1_cycle1_MsPos/Index.idx.xml: [testng] 07:22:21,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 07:22:21,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:22:21,803 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-05-19_07-22-21.log] [testng] 07:22:21,803 |-INFO in ch.qos.logback.core.sift.SiftProcessor@58758a8 - End of configuration. [testng] [2025-05-19 07:22:40,220] [pool-1-thread-7] Initializing /data/public/omer/006P_M3/006P__2017-08-19T12_42_59-Measurement 3/Images/Index.idx.xml: [testng] 07:22:40,220 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 07:22:40,220 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:22:40,221 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-05-19_07-22-40.log] [testng] 07:22:40,221 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71dcf84a - End of configuration. [testng] [2025-05-19 07:22:52,015] [pool-1-thread-6] Initializing /data/public/idr0034/HipSci Experiment 10 Plate 1__2014-08-21T17_57_35-Measurement1/Images/Index.idx.xml: [testng] 07:22:52,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 07:22:52,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:22:52,016 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-05-19_07-22-52.log] [testng] 07:22:52,016 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32c92e5f - End of configuration. [testng] [2025-05-19 07:26:03,091] [pool-1-thread-5] Initializing /data/samples/extra-directories/Index.idx.xml: [testng] 07:26:03,091 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 07:26:03,091 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:26:03,092 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-05-19_07-26-03.log] [testng] 07:26:03,092 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15615b4 - End of configuration. [testng] [2025-05-19 07:26:11,186] [pool-1-thread-4] Initializing /data/pki/DataSet/dec61bf8-5ca8-415a-8639-b75bf59ca47c/images/index.xml: [testng] 07:26:11,186 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 07:26:11,186 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:26:11,186 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-05-19_07-26-11.log] [testng] 07:26:11,187 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a96b881 - End of configuration. [testng] [2025-05-19 07:26:22,503] [pool-1-thread-3] Initializing /data/public/omer/006P_M3/006P_M3_overview_fields.png: [testng] 07:26:22,504 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 07:26:22,504 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:26:22,504 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-05-19_07-26-22.log] [testng] 07:26:22,505 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22da2784 - End of configuration. [testng] [2025-05-19 07:26:22,889] [pool-1-thread-2] Initializing /data/hms/ryang_skbr3_p1__2012-07-10T15_24_30-Measurement1/Images/Index.idx.xml: [testng] 07:26:22,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 07:26:22,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:26:22,890 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-05-19_07-26-22.log] [testng] 07:26:22,891 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5efa2094 - End of configuration. [testng] [2025-05-19 07:26:45,494] [pool-1-thread-3] Initializing /data/samples/no-first-series/Index.idx.xml: [testng] [2025-05-19 07:26:56,679] [pool-1-thread-1] Initializing /data/pki/Export/HRMNY-13786__2021-11-23T13_44_30-Measurement 3/Images/Index.xml: [testng] [2025-05-19 07:28:28,152] [pool-1-thread-11] Initializing /data/samples/32-bit-file/Index.idx.xml: [testng] [2025-05-19 07:32:51,938] [pool-1-thread-2] Initializing /data/samples/smaller-xy/Index.idx.xml: [testng] [2025-05-19 07:33:04,054] [pool-1-thread-3] Initializing /data/stephen/P004-CC Edu-pHH3__2009-02-03T17_36_29-Measurement1/Images/Index.idx.xml: [testng] 09:22:33,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 09:22:33,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:22:33,496 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-05-19_09-22-33.log] [testng] 09:22:33,496 |-INFO in ch.qos.logback.core.sift.SiftProcessor@624967f3 - End of configuration. [testng] 09:34:21,439 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 09:34:21,439 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:34:21,441 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-05-19_09-34-21.log] [testng] 09:34:21,441 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3300fee - End of configuration. [testng] 09:36:37,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 09:36:37,854 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:36:37,855 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-05-19_09-36-37.log] [testng] 09:36:37,855 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57676b11 - End of configuration. Build was aborted Calling Pipeline was cancelled Finished: ABORTED