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Started by upstream project "BIOFORMATS-test-repo" build number 130 originally caused by: Started by upstream project "Trigger" build number 147 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins15096949122999275687.sh + '[' vectra-qptiff = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_20359_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 [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] 1 warning test-automated: [testng] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 11:21:34,028 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 11:21:34,030 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 11:21:34,030 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:21:34,031 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:21:34,031 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 11:21:34,032 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 11:21:34,032 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 11:21:34,032 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:21:34,032 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:21:34,033 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 11:21:34,033 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:21:34,034 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:21:34,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:21:34,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:21:34,224 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:21:34,224 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:21:34,230 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:21:34,230 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:21:34,230 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:21:34,230 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:21:34,230 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 11:21:34,231 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 11:21:34,231 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 199 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-23 11:21:34,240] [main] java.version = 11.0.16 [testng] 11:21:34,243 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:21:34,243 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:21:34,284 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-23_11-21-34.log] [testng] 11:21:34,286 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-07-23 11:21:34,288] [main] testng.directory = /data [testng] [2024-07-23 11:21:34,288] [main] testng.configDirectory = /config [testng] [2024-07-23 11:21:34,299] [main] testng.multiplier = 1.0 [testng] [2024-07-23 11:21:34,300] [main] testng.in-memory = false [testng] [2024-07-23 11:21:34,300] [main] testng.allow-missing = false [testng] [2024-07-23 11:21:34,300] [main] user.language = en [testng] [2024-07-23 11:21:34,300] [main] user.country = ${user.country} [testng] [2024-07-23 11:21:34,300] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-23 11:21:34,810] [main] ---------------------------------------- [testng] [2024-07-23 11:21:34,810] [main] Total files: 15 [testng] [2024-07-23 11:21:34,811] [main] Scan time: 0.51 s (34 ms/file) [testng] [2024-07-23 11:21:34,811] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 14 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-23 11:21:41,399] [pool-1-thread-1] Initializing /data/public/perkinelmer/PKI_fields/LuCa-7color_[17572,60173]_3x3component_data.tif: [testng] 11:21:41,400 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 11:21:41,400 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:21:41,402 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-23_11-21-41.log] [testng] 11:21:41,402 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f433db3 - End of configuration. [testng] [2024-07-23 11:21:41,500] [pool-1-thread-12] Initializing /data/public/perkinelmer/PKI_fields/HnE_3_1x1component_data.tif: [testng] 11:21:41,501 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 11:21:41,501 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:21:41,524 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-23_11-21-41.log] [testng] 11:21:41,525 |-INFO in ch.qos.logback.core.sift.SiftProcessor@602431cf - End of configuration. [testng] [2024-07-23 11:21:41,595] [pool-1-thread-11] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch7_BC2-Section7_HP_IM3_0_[19914,7286]_component_data.tif: [testng] 11:21:41,595 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 11:21:41,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:21:41,596 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-23_11-21-41.log] [testng] 11:21:41,597 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2fdc1a62 - End of configuration. [testng] [2024-07-23 11:21:41,693] [pool-1-thread-10] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch6_BC2-Section6_HP_IM3_6_[13720,15451]_component_data.tif: [testng] 11:21:41,693 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 11:21:41,693 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:21:41,694 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-23_11-21-41.log] [testng] 11:21:41,694 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67fbeca0 - End of configuration. [testng] [2024-07-23 11:21:41,820] [pool-1-thread-9] Initializing /data/public/perkinelmer/PKI_scans/LuCa-7color_Scan1.qptiff: [testng] 11:21:41,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 11:21:41,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:21:41,821 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-23_11-21-41.log] [testng] 11:21:41,822 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65670931 - End of configuration. [testng] [2024-07-23 11:21:41,914] [pool-1-thread-8] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch7_BC2-Section7_HP_IM3_1_[15381,15412]_component_data.tif: [testng] 11:21:41,914 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 11:21:41,914 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:21:41,915 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-23_11-21-41.log] [testng] 11:21:41,915 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4409ab1d - End of configuration. [testng] [2024-07-23 11:21:41,996] [pool-1-thread-7] Initializing /data/public/perkinelmer/PKI_scans/HandEcompressed_Scan1.qptiff: [testng] 11:21:41,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 11:21:41,996 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:21:41,997 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-23_11-21-41.log] [testng] 11:21:41,997 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68ce7cc1 - End of configuration. [testng] [2024-07-23 11:21:42,058] [pool-1-thread-6] Initializing /data/perkinelmer/BreastCancer7Color_Scan1.qptiff: [testng] 11:21:42,059 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 11:21:42,059 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:21:42,059 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-23_11-21-42.log] [testng] 11:21:42,060 |-INFO in ch.qos.logback.core.sift.SiftProcessor@260baca7 - End of configuration. [testng] [2024-07-23 11:21:42,161] [pool-1-thread-5] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch8_BC2-Section16_HP_IM3_7_[19122,8127]_component_data.tif: [testng] 11:21:42,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 11:21:42,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:21:42,162 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-23_11-21-42.log] [testng] 11:21:42,163 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e7a5c8a - End of configuration. [testng] [2024-07-23 11:21:42,258] [pool-1-thread-4] Initializing /data/public/perkinelmer/PKI_fields/LuCa-7color_[13860,52919]_1x1component_data.tif: [testng] 11:21:42,259 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 11:21:42,259 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:21:42,259 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-23_11-21-42.log] [testng] 11:21:42,260 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f042255 - End of configuration. [testng] [2024-07-23 11:21:42,319] [pool-1-thread-3] Initializing /data/public/perkinelmer/PKI_fields/HandEcompressed_[11004,54205]_2x2component_data.tif: [testng] 11:21:42,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 11:21:42,320 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:21:42,320 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-23_11-21-42.log] [testng] 11:21:42,321 |-INFO in ch.qos.logback.core.sift.SiftProcessor@612dbea7 - End of configuration. [testng] [2024-07-23 11:21:42,382] [pool-1-thread-2] Initializing /data/perkinelmer/ROA-AB1_Scan1.qptiff: [testng] 11:21:42,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 11:21:42,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:21:42,384 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-23_11-21-42.log] [testng] 11:21:42,384 |-INFO in ch.qos.logback.core.sift.SiftProcessor@232b3191 - End of configuration. [testng] [2024-07-23 11:21:47,290] [pool-1-thread-5] Initializing /data/public/perkinelmer/PKI_scans/HandEuncompressed_Scan1.qptiff: [testng] [2024-07-23 11:21:47,408] [pool-1-thread-12] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch9_BC2-Section15_HP_IM3_0_[18834,16612]_component_data.tif: [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 4 seconds Finished: SUCCESS