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Started by upstream project "BIOFORMATS-test-repo" build number 277 originally caused by: Started by upstream project "Trigger" build number 298 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/jenkins8316054712476530157.sh + '[' amira = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_43639_merge_ci -v /uod/idr/repos/curated/amira:/data -v /uod/idr-scratch/merge-ci/curated/amira:/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] 00:27:28,919 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:27:28,921 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 00:27:28,921 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:27:28,922 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:27:28,922 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:27:28,923 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:27:28,923 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:27:28,923 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:27:28,924 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:27:28,925 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:27:28,926 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:27:28,926 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:27:29,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:27:29,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:27:29,144 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:27:29,144 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:27:29,150 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:27:29,150 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:27:29,150 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:27:29,151 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:27:29,151 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 00:27:29,152 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 00:27:29,152 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 228 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-03 00:27:29,161] [main] java.version = 11.0.16 [testng] 00:27:29,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:27:29,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:29,211 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-03_00-27-29.log] [testng] 00:27:29,212 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-12-03 00:27:29,214] [main] testng.directory = /data [testng] [2024-12-03 00:27:29,215] [main] testng.configDirectory = /config [testng] [2024-12-03 00:27:29,225] [main] testng.multiplier = 1.0 [testng] [2024-12-03 00:27:29,226] [main] testng.in-memory = false [testng] [2024-12-03 00:27:29,226] [main] testng.allow-missing = false [testng] [2024-12-03 00:27:29,227] [main] user.language = en [testng] [2024-12-03 00:27:29,227] [main] user.country = ${user.country} [testng] [2024-12-03 00:27:29,227] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-03 00:27:33,072] [main] ---------------------------------------- [testng] [2024-12-03 00:27:33,072] [main] Total files: 15 [testng] [2024-12-03 00:27:33,072] [main] Scan time: 3.845 s (256 ms/file) [testng] [2024-12-03 00:27:33,072] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 12 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-03 00:27:40,949] [pool-1-thread-1] Initializing /data/jeremy/Hiv_spikes.am: [testng] 00:27:40,950 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:27:40,950 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:40,952 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-03_00-27-40.log] [testng] 00:27:40,953 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66225a27 - End of configuration. [testng] [2024-12-03 00:27:41,297] [pool-1-thread-12] Initializing /data/public/imagesc-50585/BF_CheckMIB.am: [testng] 00:27:41,298 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:27:41,298 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:41,299 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-03_00-27-41.log] [testng] 00:27:41,299 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66a2ff4e - End of configuration. [testng] [2024-12-03 00:27:41,643] [pool-1-thread-11] Initializing /data/samples/emptykey/test.am: [testng] 00:27:41,643 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:27:41,643 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:41,644 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-03_00-27-41.log] [testng] 00:27:41,644 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13781e7 - End of configuration. [testng] [2024-12-03 00:27:41,958] [pool-1-thread-10] Initializing /data/jeremy/Virus_Membrane7-screenshot.PNG: [testng] 00:27:41,958 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:27:41,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:41,959 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-03_00-27-41.log] [testng] 00:27:41,960 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c7bde09 - End of configuration. [testng] [2024-12-03 00:27:41,986] [pool-1-thread-9] Initializing /data/public/imagesc-50585/BF_Check.tif: [testng] 00:27:41,987 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:27:41,987 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:41,987 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-03_00-27-41.log] [testng] 00:27:41,988 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59c48302 - End of configuration. [testng] [2024-12-03 00:27:42,821] [pool-1-thread-8] Initializing /data/ilya/test.am: [testng] 00:27:42,821 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:27:42,821 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:42,822 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-03_00-27-42.log] [testng] 00:27:42,823 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b31582d - End of configuration. [testng] [2024-12-03 00:27:43,169] [pool-1-thread-7] Initializing /data/public/imagesc-50585/BF_CheckAmira.am: [testng] 00:27:43,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:27:43,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:43,170 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-03_00-27-43.log] [testng] 00:27:43,170 |-INFO in ch.qos.logback.core.sift.SiftProcessor@260903aa - End of configuration. [testng] [2024-12-03 00:27:43,664] [pool-1-thread-6] Initializing /data/johannes/template.grey: [testng] 00:27:43,664 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:27:43,664 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:43,665 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-03_00-27-43.log] [testng] 00:27:43,665 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fb216bc - End of configuration. [testng] [2024-12-03 00:27:44,014] [pool-1-thread-5] Initializing /data/jcb/201108088/Haberman-Fig4A-original.am: [testng] 00:27:44,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:27:44,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:44,015 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-03_00-27-44.log] [testng] 00:27:44,015 |-INFO in ch.qos.logback.core.sift.SiftProcessor@629fa43d - End of configuration. [testng] [2024-12-03 00:27:44,340] [pool-1-thread-4] Initializing /data/jeremy/Virus_Membrane7.am: [testng] 00:27:44,341 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:27:44,341 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:44,341 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-03_00-27-44.log] [testng] 00:27:44,342 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a10c7ca - End of configuration. [testng] [2024-12-03 00:27:44,656] [pool-1-thread-3] Initializing /data/johannes/template.labels: [testng] 00:27:44,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:27:44,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:44,656 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-03_00-27-44.log] [testng] 00:27:44,657 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b9e0b8a - End of configuration. [testng] [2024-12-03 00:27:44,965] [pool-1-thread-2] Initializing /data/public/ignacio/test.am: [testng] 00:27:44,966 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:27:44,966 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:27:44,966 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-03_00-27-44.log] [testng] 00:27:44,967 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b529531 - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 636, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 25 seconds Finished: SUCCESS