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Started by upstream project "BIOFORMATS-test-repo" build number 297 originally caused by: Started by upstream project "Trigger" build number 319 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins12149801295023260938.sh + '[' vectra-qptiff = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_46953_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] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-mdbtools/5.3.4-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/metakit/5.3.8-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-poi/5.3.10-SNAPSHOT/maven-metadata.xml [resolver:resolve] Resolving artifacts [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-mdbtools/5.3.4-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/metakit/5.3.8-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-poi/5.3.10-SNAPSHOT/maven-metadata.xml compile-tests: [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-mdbtools/5.3.4-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/metakit/5.3.8-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-poi/5.3.10-SNAPSHOT/maven-metadata.xml [resolver:resolve] Resolving artifacts [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-mdbtools/5.3.4-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/metakit/5.3.8-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-poi/5.3.10-SNAPSHOT/maven-metadata.xml [javac] Compiling 1 source file to /bio-formats-build/bioformats/components/test-suite/test test-automated: [testng] File leak detector installed [testng] 00:41:45,900 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:41:45,902 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:41:45,902 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:41:45,903 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:41:45,903 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:41:45,903 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:41:45,903 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:41:45,903 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:41:45,904 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:41:45,904 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:41:45,904 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:41:45,904 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:41:46,127 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:41:46,127 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:41:46,153 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:41:46,153 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:41:46,161 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:41:46,161 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:41:46,161 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:41:46,161 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:41:46,161 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:41:46,162 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:41:46,162 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 258 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-24 00:41:46,172] [main] java.version = 1.8.0_342 [testng] 00:41:46,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:41:46,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:41:46,218 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-24_00-41-46.log] [testng] 00:41:46,220 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-24 00:41:46,222] [main] testng.directory = /data [testng] [2024-12-24 00:41:46,222] [main] testng.configDirectory = /config [testng] [2024-12-24 00:41:46,233] [main] testng.multiplier = 1.0 [testng] [2024-12-24 00:41:46,234] [main] testng.in-memory = false [testng] [2024-12-24 00:41:46,234] [main] testng.allow-missing = false [testng] [2024-12-24 00:41:46,234] [main] user.language = en [testng] [2024-12-24 00:41:46,234] [main] user.country = ${user.country} [testng] [2024-12-24 00:41:46,234] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-24 00:41:47,915] [main] ---------------------------------------- [testng] [2024-12-24 00:41:47,915] [main] Total files: 15 [testng] [2024-12-24 00:41:47,915] [main] Scan time: 1.681 s (112 ms/file) [testng] [2024-12-24 00:41:47,915] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 14 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-24 00:42:05,452] [pool-1-thread-1] Initializing /data/perkinelmer/ROA-AB1_Scan1.qptiff: [testng] 00:42:05,452 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:42:05,452 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:05,453 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-24_00-42-05.log] [testng] 00:42:05,453 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34b71672 - End of configuration. [testng] [2024-12-24 00:42:06,329] [pool-1-thread-12] Initializing /data/public/perkinelmer/PKI_scans/HandEuncompressed_Scan1.qptiff: [testng] 00:42:06,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:42:06,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:06,331 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-24_00-42-06.log] [testng] 00:42:06,332 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68f74eb9 - End of configuration. [testng] [2024-12-24 00:42:07,291] [pool-1-thread-11] Initializing /data/public/perkinelmer/PKI_fields/LuCa-7color_[13860,52919]_1x1component_data.tif: [testng] 00:42:07,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:42:07,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:07,293 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-24_00-42-07.log] [testng] 00:42:07,294 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7145c315 - End of configuration. [testng] [2024-12-24 00:42:08,676] [pool-1-thread-10] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch9_BC2-Section15_HP_IM3_0_[18834,16612]_component_data.tif: [testng] 00:42:08,676 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:42:08,676 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:08,677 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-24_00-42-08.log] [testng] 00:42:08,677 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40172171 - End of configuration. [testng] [2024-12-24 00:42:10,372] [pool-1-thread-9] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch7_BC2-Section7_HP_IM3_1_[15381,15412]_component_data.tif: [testng] 00:42:10,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:42:10,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:10,373 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-24_00-42-10.log] [testng] 00:42:10,373 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f07613f - End of configuration. [testng] [2024-12-24 00:42:12,182] [pool-1-thread-8] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch6_BC2-Section6_HP_IM3_6_[13720,15451]_component_data.tif: [testng] 00:42:12,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:42:12,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:12,183 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-24_00-42-12.log] [testng] 00:42:12,183 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6506494e - End of configuration. [testng] [2024-12-24 00:42:13,673] [pool-1-thread-7] Initializing /data/perkinelmer/BreastCancer7Color_Scan1.qptiff: [testng] 00:42:13,673 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:42:13,673 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:13,674 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-24_00-42-13.log] [testng] 00:42:13,674 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c12ba89 - End of configuration. [testng] [2024-12-24 00:42:14,852] [pool-1-thread-6] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch7_BC2-Section7_HP_IM3_0_[19914,7286]_component_data.tif: [testng] 00:42:14,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:42:14,852 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:14,852 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-24_00-42-14.log] [testng] 00:42:14,853 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b695f44 - End of configuration. [testng] [2024-12-24 00:42:15,717] [pool-1-thread-5] Initializing /data/public/perkinelmer/PKI_fields/LuCa-7color_[17572,60173]_3x3component_data.tif: [testng] 00:42:15,717 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:42:15,717 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:15,718 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-24_00-42-15.log] [testng] 00:42:15,718 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7bb00d6a - End of configuration. [testng] [2024-12-24 00:42:16,955] [pool-1-thread-4] Initializing /data/public/perkinelmer/PKI_fields/HnE_3_1x1component_data.tif: [testng] 00:42:16,955 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:42:16,955 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:16,956 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-24_00-42-16.log] [testng] 00:42:16,957 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10c088fa - End of configuration. [testng] [2024-12-24 00:42:17,773] [pool-1-thread-3] Initializing /data/public/perkinelmer/PKI_scans/HandEcompressed_Scan1.qptiff: [testng] 00:42:17,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:42:17,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:17,775 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-24_00-42-17.log] [testng] 00:42:17,776 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d713235 - End of configuration. [testng] [2024-12-24 00:42:18,744] [pool-1-thread-2] Initializing /data/public/perkinelmer/PKI_fields/HandEcompressed_[11004,54205]_2x2component_data.tif: [testng] 00:42:18,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:42:18,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:42:18,745 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-24_00-42-18.log] [testng] 00:42:18,746 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27722c2a - End of configuration. [testng] [2024-12-24 00:42:27,818] [pool-1-thread-6] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch8_BC2-Section16_HP_IM3_7_[19122,8127]_component_data.tif: [testng] [2024-12-24 00:42:28,441] [pool-1-thread-11] Initializing /data/public/perkinelmer/PKI_scans/LuCa-7color_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: 1 minute 19 seconds Finished: SUCCESS