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Started by upstream project "BIOFORMATS-test-repo" build number 256 originally caused by: Started by upstream project "Trigger" build number 280 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins16057436755897120104.sh + '[' vectra-qptiff = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_40350_merge_ci -v /uod/idr/repos/curated/vectra-qptiff:/data -v /uod/idr-scratch/merge-ci/curated/vectra-qptiff:/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] 00:46:24,191 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:46:24,192 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:46:24,192 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:46:24,193 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:46:24,193 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:46:24,194 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:46:24,194 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:46:24,194 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:46:24,194 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:46:24,195 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:46:24,195 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:46:24,195 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:46:24,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:46:24,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:46:24,444 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:46:24,444 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:46:24,452 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:46:24,452 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:46:24,452 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:46:24,452 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:46:24,452 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:46:24,453 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:46:24,453 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 259 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-15 00:46:24,463] [main] java.version = 1.8.0_342 [testng] 00:46:24,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:46:24,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:24,517 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-15_00-46-24.log] [testng] 00:46:24,519 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-15 00:46:24,521] [main] testng.directory = /data [testng] [2024-11-15 00:46:24,521] [main] testng.configDirectory = /config [testng] [2024-11-15 00:46:24,533] [main] testng.multiplier = 1.0 [testng] [2024-11-15 00:46:24,533] [main] testng.in-memory = false [testng] [2024-11-15 00:46:24,533] [main] testng.allow-missing = false [testng] [2024-11-15 00:46:24,533] [main] user.language = en [testng] [2024-11-15 00:46:24,533] [main] user.country = ${user.country} [testng] [2024-11-15 00:46:24,533] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-15 00:46:25,507] [main] ---------------------------------------- [testng] [2024-11-15 00:46:25,507] [main] Total files: 15 [testng] [2024-11-15 00:46:25,507] [main] Scan time: 0.974 s (64 ms/file) [testng] [2024-11-15 00:46:25,507] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 14 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-15 00:46:33,345] [pool-1-thread-1] Initializing /data/public/perkinelmer/PKI_fields/HandEcompressed_[11004,54205]_2x2component_data.tif: [testng] 00:46:33,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:46:33,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:33,346 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-15_00-46-33.log] [testng] 00:46:33,347 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e4d6bdd - End of configuration. [testng] [2024-11-15 00:46:33,626] [pool-1-thread-12] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch9_BC2-Section15_HP_IM3_0_[18834,16612]_component_data.tif: [testng] 00:46:33,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:46:33,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:33,627 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-15_00-46-33.log] [testng] 00:46:33,627 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e872022 - End of configuration. [testng] [2024-11-15 00:46:33,849] [pool-1-thread-11] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch7_BC2-Section7_HP_IM3_0_[19914,7286]_component_data.tif: [testng] 00:46:33,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:46:33,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:33,850 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-15_00-46-33.log] [testng] 00:46:33,850 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46652ac1 - End of configuration. [testng] [2024-11-15 00:46:34,147] [pool-1-thread-10] Initializing /data/perkinelmer/ROA-AB1_Scan1.qptiff: [testng] 00:46:34,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:46:34,147 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:34,148 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-15_00-46-34.log] [testng] 00:46:34,148 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b20de5e - End of configuration. [testng] [2024-11-15 00:46:34,418] [pool-1-thread-9] Initializing /data/public/perkinelmer/PKI_scans/HandEcompressed_Scan1.qptiff: [testng] 00:46:34,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:46:34,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:34,419 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-15_00-46-34.log] [testng] 00:46:34,419 |-INFO in ch.qos.logback.core.sift.SiftProcessor@797702eb - End of configuration. [testng] [2024-11-15 00:46:34,659] [pool-1-thread-8] Initializing /data/public/perkinelmer/PKI_fields/LuCa-7color_[13860,52919]_1x1component_data.tif: [testng] 00:46:34,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:46:34,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:34,660 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-15_00-46-34.log] [testng] 00:46:34,660 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e7bb1ee - End of configuration. [testng] [2024-11-15 00:46:35,003] [pool-1-thread-7] Initializing /data/public/perkinelmer/PKI_scans/LuCa-7color_Scan1.qptiff: [testng] 00:46:35,003 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:46:35,003 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:35,004 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-15_00-46-35.log] [testng] 00:46:35,004 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45422a20 - End of configuration. [testng] [2024-11-15 00:46:35,322] [pool-1-thread-6] Initializing /data/public/perkinelmer/PKI_fields/LuCa-7color_[17572,60173]_3x3component_data.tif: [testng] 00:46:35,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:46:35,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:35,323 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-15_00-46-35.log] [testng] 00:46:35,324 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29fcacfb - End of configuration. [testng] [2024-11-15 00:46:35,719] [pool-1-thread-5] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch7_BC2-Section7_HP_IM3_1_[15381,15412]_component_data.tif: [testng] 00:46:35,719 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:46:35,719 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:35,720 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-15_00-46-35.log] [testng] 00:46:35,720 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7584f855 - End of configuration. [testng] [2024-11-15 00:46:36,071] [pool-1-thread-4] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch6_BC2-Section6_HP_IM3_6_[13720,15451]_component_data.tif: [testng] 00:46:36,071 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:46:36,071 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:36,072 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-15_00-46-36.log] [testng] 00:46:36,072 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32f3a8ea - End of configuration. [testng] [2024-11-15 00:46:36,607] [pool-1-thread-3] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch8_BC2-Section16_HP_IM3_7_[19122,8127]_component_data.tif: [testng] 00:46:36,607 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:46:36,607 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:36,608 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-15_00-46-36.log] [testng] 00:46:36,608 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fc5a249 - End of configuration. [testng] [2024-11-15 00:46:37,039] [pool-1-thread-2] Initializing /data/public/perkinelmer/PKI_fields/HnE_3_1x1component_data.tif: [testng] 00:46:37,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:46:37,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:46:37,040 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-15_00-46-37.log] [testng] 00:46:37,040 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ca14f18 - End of configuration. [testng] [2024-11-15 00:46:43,317] [pool-1-thread-4] Initializing /data/public/perkinelmer/PKI_scans/HandEuncompressed_Scan1.qptiff: [testng] [2024-11-15 00:46:43,586] [pool-1-thread-3] Initializing /data/perkinelmer/BreastCancer7Color_Scan1.qptiff: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 742, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 52 seconds Finished: SUCCESS