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Started by upstream project "BIOFORMATS-test-repo" build number 1 originally caused by: Started by upstream project "Trigger" build number 1 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/jenkins14279726905164183532.sh + '[' amira = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_26_merge_ci -v /uod/idr/repos/curated/amira:/data -v /uod/idr-scratch/devspace/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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings 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] 16:01:33,403 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 16:01:33,404 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 16:01:33,404 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 16:01:33,406 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 16:01:33,406 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 16:01:33,407 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 16:01:33,407 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 16:01:33,407 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 16:01:33,408 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 16:01:33,408 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 16:01:33,409 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 16:01:33,409 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 16:01:33,583 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 16:01:33,583 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 16:01:33,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 16:01:33,611 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 16:01:33,618 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 16:01:33,618 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 16:01:33,618 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 16:01:33,619 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 16:01:33,619 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 16:01:33,620 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 16:01:33,620 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 212 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-14 16:01:33,630] [main] java.version = 21 [testng] 16:01:33,633 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 16:01:33,633 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:01:33,678 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-14_16-01-33.log] [testng] 16:01:33,680 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-03-14 16:01:33,682] [main] testng.directory = /data [testng] [2024-03-14 16:01:33,682] [main] testng.configDirectory = /config [testng] [2024-03-14 16:01:33,691] [main] testng.multiplier = 1.0 [testng] [2024-03-14 16:01:33,692] [main] testng.in-memory = false [testng] [2024-03-14 16:01:33,692] [main] testng.allow-missing = false [testng] [2024-03-14 16:01:33,692] [main] user.language = en [testng] [2024-03-14 16:01:33,692] [main] user.country = ${user.country} [testng] [2024-03-14 16:01:33,692] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-14 16:01:35,194] [main] ---------------------------------------- [testng] [2024-03-14 16:01:35,194] [main] Total files: 15 [testng] [2024-03-14 16:01:35,194] [main] Scan time: 1.502 s (100 ms/file) [testng] [2024-03-14 16:01:35,194] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 12 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-14 16:01:38,839] [pool-1-thread-1] Initializing /data/public/imagesc-50585/BF_CheckMIB.am: [testng] 16:01:38,840 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 16:01:38,840 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:01:38,842 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-14_16-01-38.log] [testng] 16:01:38,842 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29878e8e - End of configuration. [testng] [2024-03-14 16:01:38,971] [pool-1-thread-12] Initializing /data/public/imagesc-50585/BF_CheckAmira.am: [testng] 16:01:38,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 16:01:38,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:01:38,973 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-14_16-01-38.log] [testng] 16:01:38,973 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e5b9d59 - End of configuration. [testng] [2024-03-14 16:01:39,097] [pool-1-thread-11] Initializing /data/johannes/template.labels: [testng] 16:01:39,097 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 16:01:39,097 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:01:39,098 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-14_16-01-39.log] [testng] 16:01:39,098 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76786538 - End of configuration. [testng] [2024-03-14 16:01:39,233] [pool-1-thread-10] Initializing /data/jeremy/Hiv_spikes.am: [testng] 16:01:39,233 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 16:01:39,234 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:01:39,235 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-14_16-01-39.log] [testng] 16:01:39,235 |-INFO in ch.qos.logback.core.sift.SiftProcessor@591983e9 - End of configuration. [testng] [2024-03-14 16:01:39,370] [pool-1-thread-9] Initializing /data/ilya/test.am: [testng] 16:01:39,370 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 16:01:39,370 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:01:39,371 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-14_16-01-39.log] [testng] 16:01:39,371 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37e2fb0c - End of configuration. [testng] [2024-03-14 16:01:39,532] [pool-1-thread-8] Initializing /data/public/ignacio/test.am: [testng] 16:01:39,532 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 16:01:39,532 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:01:39,533 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-14_16-01-39.log] [testng] 16:01:39,533 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ca6dcdb - End of configuration. [testng] [2024-03-14 16:01:39,652] [pool-1-thread-7] Initializing /data/public/imagesc-50585/BF_Check.tif: [testng] 16:01:39,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 16:01:39,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:01:39,653 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-14_16-01-39.log] [testng] 16:01:39,653 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ee30981 - End of configuration. [testng] [2024-03-14 16:01:39,972] [pool-1-thread-6] Initializing /data/jeremy/Virus_Membrane7.am: [testng] 16:01:39,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 16:01:39,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:01:39,973 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-14_16-01-39.log] [testng] 16:01:39,973 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d1fe317 - End of configuration. [testng] [2024-03-14 16:01:40,094] [pool-1-thread-5] Initializing /data/jeremy/Virus_Membrane7-screenshot.PNG: [testng] 16:01:40,094 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 16:01:40,094 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:01:40,095 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-14_16-01-40.log] [testng] 16:01:40,095 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b6c4e05 - End of configuration. [testng] [2024-03-14 16:01:40,105] [pool-1-thread-4] Initializing /data/jcb/201108088/Haberman-Fig4A-original.am: [testng] 16:01:40,106 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 16:01:40,106 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:01:40,106 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-14_16-01-40.log] [testng] 16:01:40,106 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43145b29 - End of configuration. [testng] [2024-03-14 16:01:40,220] [pool-1-thread-3] Initializing /data/samples/emptykey/test.am: [testng] 16:01:40,220 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 16:01:40,220 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:01:40,221 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-14_16-01-40.log] [testng] 16:01:40,221 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52be6fe - End of configuration. [testng] [2024-03-14 16:01:40,330] [pool-1-thread-2] Initializing /data/johannes/template.grey: [testng] 16:01:40,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 16:01:40,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:01:40,331 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-14_16-01-40.log] [testng] 16:01:40,331 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74675abb - 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: 15 seconds Finished: SUCCESS