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Started by upstream project "BIOFORMATS-test-repo" build number 294 originally caused by: Started by upstream project "Trigger" build number 313 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins15230287598272124846.sh + '[' vectra-qptiff = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_46457_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] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 02:11:12,082 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:11:12,083 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 02:11:12,083 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:11:12,084 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:11:12,085 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:11:12,085 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:11:12,085 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:11:12,085 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:11:12,086 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:11:12,086 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:11:12,087 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:11:12,087 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:11:12,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:11:12,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:11:12,260 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:11:12,260 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:11:12,265 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:11:12,265 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:11:12,265 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:11:12,265 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:11:12,265 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 02:11:12,266 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 02:11:12,267 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 181 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-18 02:11:12,275] [main] java.version = 17.0.2 [testng] 02:11:12,278 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:11:12,278 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:11:12,316 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-18_02-11-12.log] [testng] 02:11:12,318 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-12-18 02:11:12,320] [main] testng.directory = /data [testng] [2024-12-18 02:11:12,320] [main] testng.configDirectory = /config [testng] [2024-12-18 02:11:12,328] [main] testng.multiplier = 1.0 [testng] [2024-12-18 02:11:12,329] [main] testng.in-memory = false [testng] [2024-12-18 02:11:12,329] [main] testng.allow-missing = false [testng] [2024-12-18 02:11:12,329] [main] user.language = en [testng] [2024-12-18 02:11:12,329] [main] user.country = ${user.country} [testng] [2024-12-18 02:11:12,329] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-18 02:11:20,265] [main] ---------------------------------------- [testng] [2024-12-18 02:11:20,266] [main] Total files: 15 [testng] [2024-12-18 02:11:20,266] [main] Scan time: 7.936 s (529 ms/file) [testng] [2024-12-18 02:11:20,266] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 14 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-18 02:13:05,337] [pool-1-thread-1] Initializing /data/public/perkinelmer/PKI_fields/LuCa-7color_[13860,52919]_1x1component_data.tif: [testng] 02:13:05,338 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:13:05,338 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:05,339 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-18_02-13-05.log] [testng] 02:13:05,340 |-INFO in ch.qos.logback.core.sift.SiftProcessor@606ce826 - End of configuration. [testng] [2024-12-18 02:13:08,389] [pool-1-thread-12] Initializing /data/public/perkinelmer/PKI_scans/HandEuncompressed_Scan1.qptiff: [testng] 02:13:08,389 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:13:08,389 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:08,390 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-18_02-13-08.log] [testng] 02:13:08,390 |-INFO in ch.qos.logback.core.sift.SiftProcessor@cd1c8f7 - End of configuration. [testng] [2024-12-18 02:13:12,601] [pool-1-thread-11] Initializing /data/perkinelmer/BreastCancer7Color_Scan1.qptiff: [testng] 02:13:12,602 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:13:12,602 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:12,603 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-18_02-13-12.log] [testng] 02:13:12,603 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1567868c - End of configuration. [testng] [2024-12-18 02:13:24,910] [pool-1-thread-10] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch7_BC2-Section7_HP_IM3_0_[19914,7286]_component_data.tif: [testng] 02:13:24,910 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:13:24,911 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:24,912 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-18_02-13-24.log] [testng] 02:13:24,912 |-INFO in ch.qos.logback.core.sift.SiftProcessor@787a3d7e - End of configuration. [testng] [2024-12-18 02:13:33,393] [pool-1-thread-9] Initializing /data/public/perkinelmer/PKI_fields/HnE_3_1x1component_data.tif: [testng] 02:13:33,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:13:33,393 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:33,394 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-18_02-13-33.log] [testng] 02:13:33,394 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7cd4192c - End of configuration. [testng] [2024-12-18 02:13:43,470] [pool-1-thread-8] Initializing /data/perkinelmer/ROA-AB1_Scan1.qptiff: [testng] 02:13:43,470 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:13:43,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:43,471 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-18_02-13-43.log] [testng] 02:13:43,472 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26ca7039 - End of configuration. [testng] [2024-12-18 02:13:51,873] [pool-1-thread-7] Initializing /data/public/perkinelmer/PKI_scans/LuCa-7color_Scan1.qptiff: [testng] 02:13:51,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:13:51,874 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:51,874 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-18_02-13-51.log] [testng] 02:13:51,875 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65c4b56e - End of configuration. [testng] [2024-12-18 02:13:58,322] [pool-1-thread-6] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch9_BC2-Section15_HP_IM3_0_[18834,16612]_component_data.tif: [testng] 02:13:58,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:13:58,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:58,323 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-18_02-13-58.log] [testng] 02:13:58,324 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2779be86 - End of configuration. [testng] [2024-12-18 02:14:10,700] [pool-1-thread-5] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch7_BC2-Section7_HP_IM3_1_[15381,15412]_component_data.tif: [testng] 02:14:10,700 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:14:10,700 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:14:10,701 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-18_02-14-10.log] [testng] 02:14:10,701 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7827d015 - End of configuration. [testng] [2024-12-18 02:14:22,242] [pool-1-thread-4] Initializing /data/public/perkinelmer/PKI_fields/HandEcompressed_[11004,54205]_2x2component_data.tif: [testng] 02:14:22,242 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:14:22,243 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:14:22,243 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-18_02-14-22.log] [testng] 02:14:22,243 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f50b196 - End of configuration. [testng] [2024-12-18 02:14:33,212] [pool-1-thread-3] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch6_BC2-Section6_HP_IM3_6_[13720,15451]_component_data.tif: [testng] 02:14:33,212 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:14:33,212 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:14:33,213 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-18_02-14-33.log] [testng] 02:14:33,213 |-INFO in ch.qos.logback.core.sift.SiftProcessor@416543e9 - End of configuration. [testng] [2024-12-18 02:14:44,074] [pool-1-thread-2] Initializing /data/perkinelmer/BondRx_Reproducibility__Batch8_BC2-Section16_HP_IM3_7_[19122,8127]_component_data.tif: [testng] 02:14:44,074 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:14:44,074 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:14:44,075 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-18_02-14-44.log] [testng] 02:14:44,075 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24e963b5 - End of configuration. [testng] [2024-12-18 02:16:13,046] [pool-1-thread-10] Initializing /data/public/perkinelmer/PKI_fields/LuCa-7color_[17572,60173]_3x3component_data.tif: [testng] [2024-12-18 02:16:24,589] [pool-1-thread-1] Initializing /data/public/perkinelmer/PKI_scans/HandEcompressed_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: 7 minutes 3 seconds Finished: SUCCESS