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Started by upstream project "BIOFORMATS-test-repo" build number 19 originally caused by: Started by upstream project "Trigger" build number 22 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/jenkins7345963130295793276.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_2307_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] 01:28:58,187 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:28:58,189 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 01:28:58,189 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:28:58,190 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:28:58,190 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:28:58,190 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:28:58,190 |-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] 01:28:58,190 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:28:58,191 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:28:58,191 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:28:58,191 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:28:58,191 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:28:58,411 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:28:58,411 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:28:58,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:28:58,438 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:28:58,446 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:28:58,446 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:28:58,446 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:28:58,447 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:28:58,447 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 01:28:58,448 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 01:28:58,448 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 257 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-01 01:28:58,458] [main] java.version = 1.8.0_342 [testng] 01:28:58,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:28:58,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:28:58,505 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-01_01-28-58.log] [testng] 01:28:58,507 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-04-01 01:28:58,509] [main] testng.directory = /data [testng] [2024-04-01 01:28:58,509] [main] testng.configDirectory = /config [testng] [2024-04-01 01:28:58,521] [main] testng.multiplier = 1.0 [testng] [2024-04-01 01:28:58,521] [main] testng.in-memory = false [testng] [2024-04-01 01:28:58,521] [main] testng.allow-missing = false [testng] [2024-04-01 01:28:58,521] [main] user.language = fr [testng] [2024-04-01 01:28:58,521] [main] user.country = FR [testng] [2024-04-01 01:28:58,521] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-04-01 01:30:15,347] [main] ---------------------------------------- [testng] [2024-04-01 01:30:15,348] [main] Total files: 14659 [testng] [2024-04-01 01:30:15,348] [main] Scan time: 76.826 s (5 ms/file) [testng] [2024-04-01 01:30:15,348] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-01 01:31:10,102] [pool-1-thread-1] Initializing /data/hms/ryang_skbr3_p1__2012-07-10T15_24_30-Measurement1/Images/Index.idx.xml: [testng] 01:31:10,102 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:31:10,102 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:10,104 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-01_01-31-10.log] [testng] 01:31:10,104 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a07d72e - End of configuration. [testng] [2024-04-01 01:31:10,151] [pool-1-thread-12] Initializing /data/stephen/P004-CC Edu-pHH3__2009-02-03T17_36_29-Measurement1/Images/Index.idx.xml: [testng] 01:31:10,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:31:10,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:10,152 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-01_01-31-10.log] [testng] 01:31:10,153 |-INFO in ch.qos.logback.core.sift.SiftProcessor@769cf8f - End of configuration. [testng] [2024-04-01 01:31:10,205] [pool-1-thread-11] Initializing /data/public/omer/006P_M3/006P_M3_overview.png: [testng] 01:31:10,205 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:31:10,205 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:10,206 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-01_01-31-10.log] [testng] 01:31:10,206 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47c5cd4c - End of configuration. [testng] [2024-04-01 01:31:10,215] [pool-1-thread-10] Initializing /data/pki/Export/HRMNY-13786__2021-11-23T13_44_30-Measurement 3/Images/Index.xml: [testng] 01:31:10,216 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:31:10,216 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:10,217 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-01_01-31-10.log] [testng] 01:31:10,217 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12c25415 - End of configuration. [testng] [2024-04-01 01:31:10,299] [pool-1-thread-9] Initializing /data/stephen/Plate 1(2)__2011-09-29T23_50_20-Measurement1/Images/Index.idx.xml: [testng] 01:31:10,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:31:10,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:10,300 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-01_01-31-10.log] [testng] 01:31:10,300 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a750ecc - End of configuration. [testng] [2024-04-01 01:31:10,353] [pool-1-thread-8] Initializing /data/public/omer/006P_M3/006P__2017-08-19T12_42_59-Measurement 3/Images/Index.idx.xml: [testng] 01:31:10,354 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:31:10,354 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:10,355 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-01_01-31-10.log] [testng] 01:31:10,356 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22c829ff - End of configuration. [testng] [2024-04-01 01:31:10,907] [pool-1-thread-7] Initializing /data/samples/smaller-xy/Index.idx.xml: [testng] 01:31:10,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:31:10,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:10,909 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-01_01-31-10.log] [testng] 01:31:10,909 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a54ccd9 - End of configuration. [testng] [2024-04-01 01:31:10,930] [pool-1-thread-6] Initializing /data/samples/32-bit-file/Index.idx.xml: [testng] 01:31:10,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:31:10,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:10,931 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-01_01-31-10.log] [testng] 01:31:10,932 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43ea463a - End of configuration. [testng] [2024-04-01 01:31:10,953] [pool-1-thread-5] Initializing /data/qa-17826/JLM-20170801-Operetta/Index.idx.xml: [testng] 01:31:10,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:31:10,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:10,954 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-01_01-31-10.log] [testng] 01:31:10,954 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5dc9b08b - End of configuration. [testng] [2024-04-01 01:31:10,978] [pool-1-thread-4] Initializing /data/public/idr0034/HipSci Experiment 10 Plate 1__2014-08-21T17_57_35-Measurement1/Images/Index.idx.xml: [testng] 01:31:10,982 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:31:10,982 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:10,983 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-01_01-31-10.log] [testng] 01:31:10,983 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6aadeca9 - End of configuration. [testng] [2024-04-01 01:31:12,026] [pool-1-thread-3] Initializing /data/samples/no-first-series/Index.idx.xml: [testng] 01:31:12,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:31:12,026 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:12,027 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-01_01-31-12.log] [testng] 01:31:12,028 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10b99891 - End of configuration. [testng] [2024-04-01 01:31:12,048] [pool-1-thread-2] Initializing /data/pki/DataSet/dec61bf8-5ca8-415a-8639-b75bf59ca47c/images/index.xml: [testng] 01:31:12,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:31:12,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:31:12,049 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-01_01-31-12.log] [testng] 01:31:12,050 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13ae5a1e - End of configuration. [testng] [2024-04-01 01:31:13,436] [pool-1-thread-11] Initializing /data/samples/new-phenix/original/Hiplex_run1_cycle1_MsPos/Index.idx.xml: [testng] [2024-04-01 01:31:20,628] [pool-1-thread-1] Initializing /data/samples/new-phenix/artificial-v6/Hiplex_run1_cycle1_MsPos/Index.idx.xml: [testng] [2024-04-01 01:31:23,106] [pool-1-thread-3] 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: 15 minutes 53 seconds Finished: SUCCESS