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Started by upstream project "BIOFORMATS-test-repo" build number 35 originally caused by: Started by upstream project "Trigger" build number 39 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins16063641724644765386.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_4767_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] 12:13:34,730 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 12:13:34,732 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 12:13:34,732 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:13:34,734 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:13:34,734 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 12:13:34,734 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 12:13:34,734 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 12:13:34,734 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:13:34,735 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:13:34,735 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 12:13:34,735 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 12:13:34,735 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 12:13:35,011 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 12:13:35,011 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 12:13:35,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 12:13:35,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 12:13:35,051 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 12:13:35,051 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 12:13:35,052 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 12:13:35,052 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 12:13:35,052 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 12:13:35,053 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 12:13:35,053 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 318 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-15 12:13:35,073] [main] java.version = 1.8.0_342 [testng] 12:13:35,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 12:13:35,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:13:35,152 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-15_12-13-35.log] [testng] 12:13:35,155 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-04-15 12:13:35,157] [main] testng.directory = /data [testng] [2024-04-15 12:13:35,158] [main] testng.configDirectory = /config [testng] [2024-04-15 12:13:35,173] [main] testng.multiplier = 1.0 [testng] [2024-04-15 12:13:35,174] [main] testng.in-memory = false [testng] [2024-04-15 12:13:35,174] [main] testng.allow-missing = false [testng] [2024-04-15 12:13:35,174] [main] user.language = fr [testng] [2024-04-15 12:13:35,174] [main] user.country = FR [testng] [2024-04-15 12:13:35,174] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-04-15 12:15:04,887] [main] ---------------------------------------- [testng] [2024-04-15 12:15:04,888] [main] Total files: 14659 [testng] [2024-04-15 12:15:04,888] [main] Scan time: 89.713 s (6 ms/file) [testng] [2024-04-15 12:15:04,888] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-15 12:16:02,655] [pool-1-thread-1] Initializing /data/hms/ryang_skbr3_p1__2012-07-10T15_24_30-Measurement1/Images/Index.idx.xml: [testng] 12:16:02,655 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 12:16:02,655 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:16:02,656 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-15_12-16-02.log] [testng] 12:16:02,657 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dd29479 - End of configuration. [testng] [2024-04-15 12:16:02,702] [pool-1-thread-12] Initializing /data/stephen/P004-CC Edu-pHH3__2009-02-03T17_36_29-Measurement1/Images/Index.idx.xml: [testng] 12:16:02,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 12:16:02,702 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:16:02,703 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-15_12-16-02.log] [testng] 12:16:02,703 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60e0119a - End of configuration. [testng] [2024-04-15 12:16:02,743] [pool-1-thread-11] Initializing /data/public/omer/006P_M3/006P_M3_overview.png: [testng] 12:16:02,743 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 12:16:02,743 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:16:02,744 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-15_12-16-02.log] [testng] 12:16:02,744 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f26de29 - End of configuration. [testng] [2024-04-15 12:16:02,751] [pool-1-thread-10] Initializing /data/pki/Export/HRMNY-13786__2021-11-23T13_44_30-Measurement 3/Images/Index.xml: [testng] 12:16:02,751 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 12:16:02,751 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:16:02,752 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-15_12-16-02.log] [testng] 12:16:02,753 |-INFO in ch.qos.logback.core.sift.SiftProcessor@168d8eb6 - End of configuration. [testng] [2024-04-15 12:16:02,832] [pool-1-thread-9] Initializing /data/stephen/Plate 1(2)__2011-09-29T23_50_20-Measurement1/Images/Index.idx.xml: [testng] 12:16:02,832 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 12:16:02,832 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:16:02,833 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-15_12-16-02.log] [testng] 12:16:02,833 |-INFO in ch.qos.logback.core.sift.SiftProcessor@656f1568 - End of configuration. [testng] [2024-04-15 12:16:02,879] [pool-1-thread-8] Initializing /data/public/omer/006P_M3/006P__2017-08-19T12_42_59-Measurement 3/Images/Index.idx.xml: [testng] 12:16:02,879 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 12:16:02,879 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:16:02,880 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-15_12-16-02.log] [testng] 12:16:02,880 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f67181a - End of configuration. [testng] [2024-04-15 12:16:03,309] [pool-1-thread-7] Initializing /data/samples/smaller-xy/Index.idx.xml: [testng] 12:16:03,310 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 12:16:03,310 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:16:03,312 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-15_12-16-03.log] [testng] 12:16:03,312 |-INFO in ch.qos.logback.core.sift.SiftProcessor@595efc6f - End of configuration. [testng] [2024-04-15 12:16:03,335] [pool-1-thread-6] Initializing /data/samples/32-bit-file/Index.idx.xml: [testng] 12:16:03,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 12:16:03,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:16:03,336 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-15_12-16-03.log] [testng] 12:16:03,337 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3431f982 - End of configuration. [testng] [2024-04-15 12:16:03,357] [pool-1-thread-5] Initializing /data/qa-17826/JLM-20170801-Operetta/Index.idx.xml: [testng] 12:16:03,357 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 12:16:03,357 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:16:03,358 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-15_12-16-03.log] [testng] 12:16:03,358 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b8a7980 - End of configuration. [testng] [2024-04-15 12:16:03,383] [pool-1-thread-4] Initializing /data/public/idr0034/HipSci Experiment 10 Plate 1__2014-08-21T17_57_35-Measurement1/Images/Index.idx.xml: [testng] 12:16:03,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 12:16:03,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:16:03,384 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-15_12-16-03.log] [testng] 12:16:03,384 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d4008dd - End of configuration. [testng] [2024-04-15 12:16:04,457] [pool-1-thread-3] Initializing /data/samples/no-first-series/Index.idx.xml: [testng] 12:16:04,457 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 12:16:04,457 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:16:04,458 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-15_12-16-04.log] [testng] 12:16:04,459 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ce00860 - End of configuration. [testng] [2024-04-15 12:16:04,482] [pool-1-thread-2] Initializing /data/pki/DataSet/dec61bf8-5ca8-415a-8639-b75bf59ca47c/images/index.xml: [testng] 12:16:04,482 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 12:16:04,482 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:16:04,482 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-15_12-16-04.log] [testng] 12:16:04,483 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47e4fe76 - End of configuration. [testng] [2024-04-15 12:16:05,797] [pool-1-thread-11] Initializing /data/samples/new-phenix/original/Hiplex_run1_cycle1_MsPos/Index.idx.xml: [testng] [2024-04-15 12:16:11,873] [pool-1-thread-1] Initializing /data/samples/new-phenix/artificial-v6/Hiplex_run1_cycle1_MsPos/Index.idx.xml: [testng] [2024-04-15 12:16:13,650] [pool-1-thread-7] Initializing /data/public/omer/006P_M3/006P_M3_overview_fields.png: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 795, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 16 minutes 9 seconds Finished: SUCCESS