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Started by upstream project "BIOFORMATS-test-repo" build number 300 originally caused by: Started by upstream project "Trigger" build number 322 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/jenkins15039775792797403185.sh + '[' vectra-qptiff = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_47448_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] 00:55:19,567 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:55:19,568 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:55:19,568 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:55:19,569 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:55:19,570 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:55:19,570 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:55:19,570 |-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] 00:55:19,570 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:55:19,571 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:55:19,571 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:55:19,571 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:55:19,571 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:55:19,799 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:55:19,799 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:55:19,826 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:55:19,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:55:19,835 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:55:19,835 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:55:19,835 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:55:19,836 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:55:19,836 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:55:19,837 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:55:19,837 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 266 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-27 00:55:19,847] [main] java.version = 1.8.0_342 [testng] 00:55:19,850 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:55:19,850 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:19,895 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-27_00-55-19.log] [testng] 00:55:19,896 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-27 00:55:19,898] [main] testng.directory = /data [testng] [2024-12-27 00:55:19,898] [main] testng.configDirectory = /config [testng] [2024-12-27 00:55:19,910] [main] testng.multiplier = 1.0 [testng] [2024-12-27 00:55:19,911] [main] testng.in-memory = false [testng] [2024-12-27 00:55:19,911] [main] testng.allow-missing = false [testng] [2024-12-27 00:55:19,911] [main] user.language = en [testng] [2024-12-27 00:55:19,911] [main] user.country = ${user.country} [testng] [2024-12-27 00:55:19,911] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-27 00:55:21,307] [main] ---------------------------------------- [testng] [2024-12-27 00:55:21,307] [main] Total files: 15 [testng] [2024-12-27 00:55:21,308] [main] Scan time: 1.396 s (93 ms/file) [testng] [2024-12-27 00:55:21,308] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 14 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-27 00:55:37,712] [pool-1-thread-1] Initializing /data/perkinelmer/ROA-AB1_Scan1.qptiff: [testng] 00:55:37,713 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:55:37,713 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:37,714 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-27_00-55-37.log] [testng] 00:55:37,714 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ddef359 - End of configuration. [testng] [2024-12-27 00:55:38,394] [pool-1-thread-12] Initializing /data/public/perkinelmer/PKI_scans/HandEuncompressed_Scan1.qptiff: [testng] 00:55:38,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:55:38,395 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:38,395 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-27_00-55-38.log] [testng] 00:55:38,396 |-INFO in ch.qos.logback.core.sift.SiftProcessor@aa1f6b7 - End of configuration. [testng] [2024-12-27 00:55:38,897] [pool-1-thread-11] Initializing /data/public/perkinelmer/PKI_fields/LuCa-7color_[13860,52919]_1x1component_data.tif: [testng] 00:55:38,898 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:55:38,898 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:38,899 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-27_00-55-38.log] [testng] 00:55:38,900 |-INFO in ch.qos.logback.core.sift.SiftProcessor@249878e8 - End of configuration. [testng] [2024-12-27 00:55:39,581] [pool-1-thread-10] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch9_BC2-Section15_HP_IM3_0_[18834,16612]_component_data.tif: [testng] 00:55:39,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:55:39,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:39,582 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-27_00-55-39.log] [testng] 00:55:39,582 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74a3b553 - End of configuration. [testng] [2024-12-27 00:55:40,146] [pool-1-thread-9] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch7_BC2-Section7_HP_IM3_1_[15381,15412]_component_data.tif: [testng] 00:55:40,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:55:40,146 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:40,147 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-27_00-55-40.log] [testng] 00:55:40,147 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2df5cdc3 - End of configuration. [testng] [2024-12-27 00:55:40,791] [pool-1-thread-8] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch6_BC2-Section6_HP_IM3_6_[13720,15451]_component_data.tif: [testng] 00:55:40,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:55:40,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:40,792 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-27_00-55-40.log] [testng] 00:55:40,792 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4de9a921 - End of configuration. [testng] [2024-12-27 00:55:41,414] [pool-1-thread-7] Initializing /data/perkinelmer/BreastCancer7Color_Scan1.qptiff: [testng] 00:55:41,415 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:55:41,415 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:41,415 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-27_00-55-41.log] [testng] 00:55:41,416 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ad47c4a - End of configuration. [testng] [2024-12-27 00:55:42,093] [pool-1-thread-6] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch7_BC2-Section7_HP_IM3_0_[19914,7286]_component_data.tif: [testng] 00:55:42,094 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:55:42,094 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:42,095 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-27_00-55-42.log] [testng] 00:55:42,095 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e13e17a - End of configuration. [testng] [2024-12-27 00:55:43,108] [pool-1-thread-5] Initializing /data/public/perkinelmer/PKI_fields/LuCa-7color_[17572,60173]_3x3component_data.tif: [testng] 00:55:43,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:55:43,108 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:43,109 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-27_00-55-43.log] [testng] 00:55:43,109 |-INFO in ch.qos.logback.core.sift.SiftProcessor@447b9eaf - End of configuration. [testng] [2024-12-27 00:55:43,680] [pool-1-thread-4] Initializing /data/public/perkinelmer/PKI_fields/HnE_3_1x1component_data.tif: [testng] 00:55:43,680 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:55:43,680 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:43,681 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-27_00-55-43.log] [testng] 00:55:43,682 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40172171 - End of configuration. [testng] [2024-12-27 00:55:44,247] [pool-1-thread-3] Initializing /data/public/perkinelmer/PKI_scans/HandEcompressed_Scan1.qptiff: [testng] 00:55:44,247 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:55:44,247 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:44,247 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-27_00-55-44.log] [testng] 00:55:44,248 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a05f81b - End of configuration. [testng] [2024-12-27 00:55:45,052] [pool-1-thread-2] Initializing /data/public/perkinelmer/PKI_fields/HandEcompressed_[11004,54205]_2x2component_data.tif: [testng] 00:55:45,052 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:55:45,053 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:45,053 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-27_00-55-45.log] [testng] 00:55:45,054 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a243b3d - End of configuration. [testng] [2024-12-27 00:55:54,679] [pool-1-thread-10] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch8_BC2-Section16_HP_IM3_7_[19122,8127]_component_data.tif: [testng] [2024-12-27 00:55:55,375] [pool-1-thread-4] 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 10 seconds Finished: SUCCESS