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Started by upstream project "BIOFORMATS-test-repo" build number 66 originally caused by: Started by upstream project "Trigger" build number 74 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins12620384322105692599.sh + '[' bruker = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_9948_merge_ci -v /uod/idr/repos/curated/bruker:/data -v /uod/idr-scratch/merge-ci/curated/bruker:/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] 09:11:04,221 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 09:11:04,223 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 09:11:04,223 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:11:04,224 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 09:11:04,224 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 09:11:04,224 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 09:11:04,225 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 09:11:04,225 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:11:04,225 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 09:11:04,225 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 09:11:04,226 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 09:11:04,226 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 09:11:04,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 09:11:04,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 09:11:04,478 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 09:11:04,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 09:11:04,488 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 09:11:04,488 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 09:11:04,488 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 09:11:04,488 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 09:11:04,488 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 09:11:04,489 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 09:11:04,489 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 264 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-17 09:11:04,499] [main] java.version = 1.8.0_342 [testng] 09:11:04,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 09:11:04,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:11:04,552 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-17_09-11-04.log] [testng] 09:11:04,554 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-05-17 09:11:04,556] [main] testng.directory = /data [testng] [2024-05-17 09:11:04,556] [main] testng.configDirectory = /config [testng] [2024-05-17 09:11:04,568] [main] testng.multiplier = 1.0 [testng] [2024-05-17 09:11:04,568] [main] testng.in-memory = false [testng] [2024-05-17 09:11:04,568] [main] testng.allow-missing = false [testng] [2024-05-17 09:11:04,568] [main] user.language = en [testng] [2024-05-17 09:11:04,569] [main] user.country = ${user.country} [testng] [2024-05-17 09:11:04,569] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-05-17 09:11:48,276] [main] ---------------------------------------- [testng] [2024-05-17 09:11:48,276] [main] Total files: 826 [testng] [2024-05-17 09:11:48,276] [main] Scan time: 43.707 s (52 ms/file) [testng] [2024-05-17 09:11:48,276] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-17 09:11:52,011] [pool-1-thread-1] Initializing /data/wis/tiffs/RA_060110_051_scan6_slice5.tif: [testng] 09:11:52,012 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 09:11:52,012 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:11:52,013 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-17_09-11-52.log] [testng] 09:11:52,014 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d69f08d - End of configuration. [testng] [2024-05-17 09:11:52,065] [pool-1-thread-12] Initializing /data/wis/tiffs/hd111104p3_sH3_scan1_slice1.tif: [testng] 09:11:52,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 09:11:52,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:11:52,066 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-17_09-11-52.log] [testng] 09:11:52,067 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e4e9635 - End of configuration. [testng] [2024-05-17 09:11:52,115] [pool-1-thread-11] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice1.tif: [testng] 09:11:52,115 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 09:11:52,115 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:11:52,116 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-17_09-11-52.log] [testng] 09:11:52,116 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f888f5f - End of configuration. [testng] [2024-05-17 09:11:52,171] [pool-1-thread-10] Initializing /data/wis/RA_060110.051/1/acqp: [testng] 09:11:52,171 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 09:11:52,171 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:11:52,172 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-17_09-11-52.log] [testng] 09:11:52,173 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48de7e5e - End of configuration. [testng] [2024-05-17 09:11:52,263] [pool-1-thread-9] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo6.tif: [testng] 09:11:52,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 09:11:52,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:11:52,264 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-17_09-11-52.log] [testng] 09:11:52,265 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3fc1e1a9 - End of configuration. [testng] [2024-05-17 09:11:52,301] [pool-1-thread-8] Initializing /data/wis/RA_240912_m1.g71/1/acqp: [testng] 09:11:52,301 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 09:11:52,301 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:11:52,302 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-17_09-11-52.log] [testng] 09:11:52,302 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39312dd8 - End of configuration. [testng] [2024-05-17 09:11:52,408] [pool-1-thread-7] Initializing /data/wis/tiffs/RAf_100110_091_Scan6_Slice5_echo1.tif: [testng] 09:11:52,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 09:11:52,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:11:52,409 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-17_09-11-52.log] [testng] 09:11:52,409 |-INFO in ch.qos.logback.core.sift.SiftProcessor@795bb30f - End of configuration. [testng] [2024-05-17 09:11:52,445] [pool-1-thread-6] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice1.tif: [testng] 09:11:52,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 09:11:52,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:11:52,446 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-17_09-11-52.log] [testng] 09:11:52,446 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7bebccbb - End of configuration. [testng] [2024-05-17 09:11:52,482] [pool-1-thread-5] Initializing /data/wis/tiffs/RA_060110_051_scan2_slice6.tif: [testng] 09:11:52,483 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 09:11:52,483 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:11:52,484 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-17_09-11-52.log] [testng] 09:11:52,484 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12d8ebe0 - End of configuration. [testng] [2024-05-17 09:11:52,522] [pool-1-thread-4] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice3.tif: [testng] 09:11:52,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 09:11:52,523 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:11:52,523 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-17_09-11-52.log] [testng] 09:11:52,523 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b7eaad6 - End of configuration. [testng] [2024-05-17 09:11:52,564] [pool-1-thread-3] Initializing /data/samples/dimension-mismatch/1/acqp: [testng] 09:11:52,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 09:11:52,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:11:52,565 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-17_09-11-52.log] [testng] 09:11:52,565 |-INFO in ch.qos.logback.core.sift.SiftProcessor@417b6328 - End of configuration. [testng] [2024-05-17 09:11:52,589] [pool-1-thread-2] Initializing /data/wis/tiffs/hd111104p3_sH3_scan5_slice1.tif: [testng] 09:11:52,589 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 09:11:52,589 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 09:11:52,590 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-17_09-11-52.log] [testng] 09:11:52,591 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b564aa2 - End of configuration. [testng] [2024-05-17 09:11:54,195] [pool-1-thread-3] Initializing /data/wis/tiffs/RAf_100110_091_Scan7_Slice9_TR6.tif: [testng] [2024-05-17 09:11:54,236] [pool-1-thread-11] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice3.tif: [testng] [2024-05-17 09:11:54,552] [pool-1-thread-5] Initializing /data/wis/tiffs/RAf_100110_091_Scan3_Slice5.tif: [testng] [2024-05-17 09:11:54,603] [pool-1-thread-7] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo1.tif: [testng] [2024-05-17 09:11:54,669] [pool-1-thread-2] Initializing /data/wis/tiffs/RAf_100110_091_Scan8_Slice9_diff15.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 901, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 1 minute 8 seconds Finished: SUCCESS