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Started by upstream project "BIOFORMATS-test-repo" build number 367 originally caused by: Started by upstream project "Trigger" build number 393 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/jenkins1635916750161977413.sh + '[' perkinelmer-operetta = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_58497_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 test-automated: [testng] File leak detector installed [testng] 00:57:05,095 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:57:05,097 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - No custom configurators were discovered as a service. [testng] 00:57:05,097 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:57:05,098 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:57:05,098 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:57:05,099 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:57:05,099 |-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] 00:57:05,099 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:57:05,099 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:57:05,100 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:57:05,100 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:57:05,100 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:57:05,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:57:05,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:57:05,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:57:05,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:57:05,372 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:57:05,372 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:57:05,372 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:57:05,373 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:57:05,373 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@63355449 - End of configuration. [testng] 00:57:05,374 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48ae9b55 - Registering current configuration as safe fallback point [testng] 00:57:05,374 |-INFO in ch.qos.logback.classic.util.ContextInitializer@7ff95560 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 275 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-07 00:57:05,384] [main] java.version = 1.8.0_342 [testng] 00:57:05,388 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:57:05,388 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:05,448 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-07_00-57-05.log] [testng] 00:57:05,456 |-INFO in ch.qos.logback.core.sift.SiftProcessor@765d7657 - End of configuration. [testng] [2025-03-07 00:57:05,461] [main] testng.directory = /data [testng] [2025-03-07 00:57:05,461] [main] testng.configDirectory = /config [testng] [2025-03-07 00:57:05,477] [main] testng.multiplier = 1.0 [testng] [2025-03-07 00:57:05,478] [main] testng.in-memory = false [testng] [2025-03-07 00:57:05,478] [main] testng.allow-missing = false [testng] [2025-03-07 00:57:05,478] [main] user.language = en [testng] [2025-03-07 00:57:05,478] [main] user.country = ${user.country} [testng] [2025-03-07 00:57:05,478] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2025-03-07 01:10:16,463] [main] ---------------------------------------- [testng] [2025-03-07 01:10:16,463] [main] Total files: 14681 [testng] [2025-03-07 01:10:16,464] [main] Scan time: 790.985 s (53 ms/file) [testng] [2025-03-07 01:10:16,464] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-07 01:33:39,651] [pool-1-thread-1] Initializing /data/samples/extra-directories/Index.idx.xml: [testng] 01:33:39,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:33:39,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:39,653 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-07_01-33-39.log] [testng] 01:33:39,653 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fb5e266 - End of configuration. [testng] [2025-03-07 01:33:41,300] [pool-1-thread-12] Initializing /data/pki/DataSet/dec61bf8-5ca8-415a-8639-b75bf59ca47c/images/index.xml: [testng] 01:33:41,300 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:33:41,300 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:41,301 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-07_01-33-41.log] [testng] 01:33:41,302 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7fb278b6 - End of configuration. [testng] [2025-03-07 01:33:43,600] [pool-1-thread-11] Initializing /data/samples/smaller-xy/Index.idx.xml: [testng] 01:33:43,600 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:33:43,601 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:43,601 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-07_01-33-43.log] [testng] 01:33:43,602 |-INFO in ch.qos.logback.core.sift.SiftProcessor@99f30d - End of configuration. [testng] [2025-03-07 01:33:45,398] [pool-1-thread-10] Initializing /data/public/idr0034/HipSci Experiment 10 Plate 1__2014-08-21T17_57_35-Measurement1/Images/Index.idx.xml: [testng] 01:33:45,398 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:33:45,398 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:33:45,399 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-07_01-33-45.log] [testng] 01:33:45,399 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26e13217 - End of configuration. [testng] [2025-03-07 01:34:25,090] [pool-1-thread-9] Initializing /data/samples/new-phenix/original/Hiplex_run1_cycle1_MsPos/Index.idx.xml: [testng] 01:34:25,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:34:25,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:25,091 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-07_01-34-25.log] [testng] 01:34:25,091 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d522528 - End of configuration. [testng] [2025-03-07 01:34:35,952] [pool-1-thread-8] Initializing /data/samples/32-bit-file/Index.idx.xml: [testng] 01:34:35,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:34:35,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:35,954 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-07_01-34-35.log] [testng] 01:34:35,954 |-INFO in ch.qos.logback.core.sift.SiftProcessor@701bbf20 - End of configuration. [testng] [2025-03-07 01:34:38,440] [pool-1-thread-7] Initializing /data/public/omer/006P_M3/006P_M3_overview.png: [testng] 01:34:38,440 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:34:38,440 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:38,441 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-07_01-34-38.log] [testng] 01:34:38,441 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f203716 - End of configuration. [testng] [2025-03-07 01:34:38,591] [pool-1-thread-6] Initializing /data/pki/Export/HRMNY-13786__2021-11-23T13_44_30-Measurement 3/Images/Index.xml: [testng] 01:34:38,591 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:34:38,591 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:38,592 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-07_01-34-38.log] [testng] 01:34:38,592 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f26de29 - End of configuration. [testng] [2025-03-07 01:34:41,722] [pool-1-thread-5] Initializing /data/stephen/Plate 1(2)__2011-09-29T23_50_20-Measurement1/Images/Index.idx.xml: [testng] 01:34:41,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:34:41,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:41,723 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-07_01-34-41.log] [testng] 01:34:41,723 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ab73a86 - End of configuration. [testng] [2025-03-07 01:34:44,212] [pool-1-thread-4] Initializing /data/public/zenodo-7841360/Hoechst__2023-03-07T10_17_54-Measurement 2/Images/Index.idx.xml: [testng] 01:34:44,213 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:34:44,213 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:44,213 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-07_01-34-44.log] [testng] 01:34:44,214 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76d54a97 - End of configuration. [testng] [2025-03-07 01:34:46,142] [pool-1-thread-3] Initializing /data/samples/new-phenix/artificial-v6/Hiplex_run1_cycle1_MsPos/Index.idx.xml: [testng] 01:34:46,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:34:46,143 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:46,143 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-07_01-34-46.log] [testng] 01:34:46,144 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a8b0dee - End of configuration. [testng] [2025-03-07 01:34:56,793] [pool-1-thread-2] Initializing /data/public/omer/006P_M3/006P__2017-08-19T12_42_59-Measurement 3/Images/Index.idx.xml: [testng] 01:34:56,794 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:34:56,794 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:34:56,794 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-07_01-34-56.log] [testng] 01:34:56,795 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a524b4a - End of configuration. [testng] [2025-03-07 01:35:06,002] [pool-1-thread-7] Initializing /data/samples/no-first-series/Index.idx.xml: [testng] [2025-03-07 01:35:31,216] [pool-1-thread-4] Initializing /data/qa-17826/JLM-20170801-Operetta/Index.idx.xml: [testng] [2025-03-07 01:37:07,841] [pool-1-thread-7] Initializing /data/stephen/P004-CC Edu-pHH3__2009-02-03T17_36_29-Measurement1/Images/Index.idx.xml: [testng] [2025-03-07 01:37:14,586] [pool-1-thread-11] Initializing /data/hms/ryang_skbr3_p1__2012-07-10T15_24_30-Measurement1/Images/Index.idx.xml: [testng] [2025-03-07 01:37:17,362] [pool-1-thread-8] Initializing /data/public/omer/006P_M3/006P_M3_overview_fields.png: [testng] 06:26:01,023 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 06:26:01,023 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:26:01,024 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-07_06-26-01.log] [testng] 06:26:01,025 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4170da0f - End of configuration. [testng] 08:03:07,130 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 08:03:07,130 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:03:07,133 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-07_08-03-07.log] [testng] 08:03:07,133 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f0011c1 - End of configuration. [testng] 08:03:16,555 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 08:03:16,555 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:03:16,557 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-07_08-03-16.log] [testng] 08:03:16,557 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3cf18b7c - End of configuration. [testng] 08:04:18,357 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 08:04:18,357 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:04:18,358 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-07_08-04-18.log] [testng] 08:04:18,360 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ab26d65 - 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: 427 minutes 16 seconds Finished: SUCCESS