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Started by upstream project "BIOFORMATS-test-repo" build number 258 originally caused by: Started by upstream project "Trigger" build number 282 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins1596936868881481131.sh + '[' perkinelmer-operetta = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_40667_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] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 00:38:49,145 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:38:49,147 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:38:49,147 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:38:49,148 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:38:49,148 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:38:49,148 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:38:49,149 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:38:49,149 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:38:49,149 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:38:49,150 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:38:49,150 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:38:49,150 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:38:49,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:38:49,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:38:49,341 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:38:49,341 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:38:49,346 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:38:49,347 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:38:49,347 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:38:49,347 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:38:49,347 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:38:49,348 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:38:49,348 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 199 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-17 00:38:49,357] [main] java.version = 17.0.2 [testng] 00:38:49,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:38:49,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:38:49,402 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-17_00-38-49.log] [testng] 00:38:49,404 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-11-17 00:38:49,407] [main] testng.directory = /data [testng] [2024-11-17 00:38:49,407] [main] testng.configDirectory = /config [testng] [2024-11-17 00:38:49,416] [main] testng.multiplier = 1.0 [testng] [2024-11-17 00:38:49,417] [main] testng.in-memory = false [testng] [2024-11-17 00:38:49,417] [main] testng.allow-missing = false [testng] [2024-11-17 00:38:49,417] [main] user.language = en [testng] [2024-11-17 00:38:49,417] [main] user.country = ${user.country} [testng] [2024-11-17 00:38:49,417] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-17 00:45:03,091] [main] ---------------------------------------- [testng] [2024-11-17 00:45:03,091] [main] Total files: 14681 [testng] [2024-11-17 00:45:03,092] [main] Scan time: 373.674 s (25 ms/file) [testng] [2024-11-17 00:45:03,092] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-17 00:47:50,655] [pool-1-thread-1] Initializing /data/qa-17826/JLM-20170801-Operetta/Index.idx.xml: [testng] 00:47:50,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:47:50,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:50,658 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-17_00-47-50.log] [testng] 00:47:50,658 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6395e547 - End of configuration. [testng] [2024-11-17 00:47:50,770] [pool-1-thread-12] Initializing /data/public/idr0034/HipSci Experiment 10 Plate 1__2014-08-21T17_57_35-Measurement1/Images/Index.idx.xml: [testng] 00:47:50,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:47:50,770 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:50,772 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-17_00-47-50.log] [testng] 00:47:50,772 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19b57930 - End of configuration. [testng] [2024-11-17 00:47:54,109] [pool-1-thread-11] Initializing /data/stephen/Plate 1(2)__2011-09-29T23_50_20-Measurement1/Images/Index.idx.xml: [testng] 00:47:54,109 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:47:54,109 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:54,110 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-17_00-47-54.log] [testng] 00:47:54,111 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c1dea8 - End of configuration. [testng] [2024-11-17 00:47:54,242] [pool-1-thread-10] Initializing /data/stephen/P004-CC Edu-pHH3__2009-02-03T17_36_29-Measurement1/Images/Index.idx.xml: [testng] 00:47:54,242 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:47:54,242 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:54,242 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-17_00-47-54.log] [testng] 00:47:54,243 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25fcc786 - End of configuration. [testng] [2024-11-17 00:47:54,746] [pool-1-thread-9] Initializing /data/samples/32-bit-file/Index.idx.xml: [testng] 00:47:54,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:47:54,746 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:54,751 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-17_00-47-54.log] [testng] 00:47:54,751 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51ffc66a - End of configuration. [testng] [2024-11-17 00:47:54,932] [pool-1-thread-8] Initializing /data/hms/ryang_skbr3_p1__2012-07-10T15_24_30-Measurement1/Images/Index.idx.xml: [testng] 00:47:54,932 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:47:54,932 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:54,933 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-17_00-47-54.log] [testng] 00:47:54,933 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ac9189b - End of configuration. [testng] [2024-11-17 00:47:55,232] [pool-1-thread-7] Initializing /data/public/omer/006P_M3/006P__2017-08-19T12_42_59-Measurement 3/Images/Index.idx.xml: [testng] 00:47:55,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:47:55,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:55,233 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-17_00-47-55.log] [testng] 00:47:55,233 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c2eaf8f - End of configuration. [testng] [2024-11-17 00:47:56,250] [pool-1-thread-6] Initializing /data/public/omer/006P_M3/006P_M3_overview.png: [testng] 00:47:56,250 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:47:56,250 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:56,251 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-17_00-47-56.log] [testng] 00:47:56,260 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5bf01ab3 - End of configuration. [testng] [2024-11-17 00:47:56,284] [pool-1-thread-5] Initializing /data/public/zenodo-7841360/Hoechst__2023-03-07T10_17_54-Measurement 2/Images/Index.idx.xml: [testng] 00:47:56,284 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:47:56,284 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:56,284 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-17_00-47-56.log] [testng] 00:47:56,285 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11486c30 - End of configuration. [testng] [2024-11-17 00:47:56,504] [pool-1-thread-4] Initializing /data/pki/DataSet/dec61bf8-5ca8-415a-8639-b75bf59ca47c/images/index.xml: [testng] 00:47:56,504 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:47:56,504 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:56,505 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-17_00-47-56.log] [testng] 00:47:56,506 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b0acfc9 - End of configuration. [testng] [2024-11-17 00:47:57,050] [pool-1-thread-3] Initializing /data/samples/new-phenix/artificial-v6/Hiplex_run1_cycle1_MsPos/Index.idx.xml: [testng] 00:47:57,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:47:57,051 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:57,051 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-17_00-47-57.log] [testng] 00:47:57,051 |-INFO in ch.qos.logback.core.sift.SiftProcessor@183b1266 - End of configuration. [testng] [2024-11-17 00:47:57,522] [pool-1-thread-2] Initializing /data/pki/Export/HRMNY-13786__2021-11-23T13_44_30-Measurement 3/Images/Index.xml: [testng] 00:47:57,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:47:57,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:57,523 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-17_00-47-57.log] [testng] 00:47:57,524 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3bd11776 - End of configuration. [testng] [2024-11-17 00:47:58,953] [pool-1-thread-6] Initializing /data/public/omer/006P_M3/006P_M3_overview_fields.png: [testng] [2024-11-17 00:47:59,759] [pool-1-thread-6] Initializing /data/samples/new-phenix/original/Hiplex_run1_cycle1_MsPos/Index.idx.xml: [testng] [2024-11-17 00:48:01,834] [pool-1-thread-5] Initializing /data/samples/smaller-xy/Index.idx.xml: [testng] [2024-11-17 00:48:15,633] [pool-1-thread-8] Initializing /data/samples/extra-directories/Index.idx.xml: [testng] [2024-11-17 00:48:17,949] [pool-1-thread-1] Initializing /data/samples/no-first-series/Index.idx.xml: [testng] 02:25:35,906 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:25:35,906 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:25:35,907 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-17_02-25-35.log] [testng] 02:25:35,907 |-INFO in ch.qos.logback.core.sift.SiftProcessor@490b4f58 - End of configuration. [testng] 02:35:29,566 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:35:29,566 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:29,568 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-17_02-35-29.log] [testng] 02:35:29,568 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1112e068 - End of configuration. [testng] 02:35:32,860 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:35:32,860 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:32,861 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-17_02-35-32.log] [testng] 02:35:32,861 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ef65658 - End of configuration. [testng] 02:35:53,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:35:53,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:35:53,724 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-17_02-35-53.log] [testng] 02:35:53,724 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76cd9333 - 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: 117 minutes 9 seconds Finished: SUCCESS