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Started by upstream project "BIOFORMATS-test-repo" build number 135 originally caused by: Started by upstream project "Trigger" build number 155 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@10 [BIOFORMATS-test-folder@10] $ /bin/bash -xe /tmp/jenkins11883868248073506344.sh + '[' imaris = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_21246_merge_ci -v /uod/idr/repos/curated/imaris:/data -v /uod/idr-scratch/merge-ci/curated/imaris:/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] 02:09:06,023 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:09:06,024 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 02:09:06,024 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:09:06,025 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:09:06,025 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:09:06,026 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:09:06,026 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:09:06,026 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:09:06,027 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:09:06,027 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:09:06,028 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:09:06,028 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:09:06,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:09:06,192 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:09:06,214 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:09:06,214 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:09:06,219 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:09:06,219 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:09:06,219 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:09:06,220 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:09:06,220 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 02:09:06,221 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 02:09:06,221 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 194 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-28 02:09:06,230] [main] java.version = 17.0.2 [testng] 02:09:06,233 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:09:06,233 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:06,274 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-28_02-09-06.log] [testng] 02:09:06,276 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-07-28 02:09:06,278] [main] testng.directory = /data [testng] [2024-07-28 02:09:06,278] [main] testng.configDirectory = /config [testng] [2024-07-28 02:09:06,287] [main] testng.multiplier = 1.0 [testng] [2024-07-28 02:09:06,288] [main] testng.in-memory = false [testng] [2024-07-28 02:09:06,288] [main] testng.allow-missing = false [testng] [2024-07-28 02:09:06,288] [main] user.language = en [testng] [2024-07-28 02:09:06,288] [main] user.country = ${user.country} [testng] [2024-07-28 02:09:06,288] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-28 02:09:13,458] [main] ---------------------------------------- [testng] [2024-07-28 02:09:13,459] [main] Total files: 68 [testng] [2024-07-28 02:09:13,459] [main] Scan time: 7.169 s (105 ms/file) [testng] [2024-07-28 02:09:13,459] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 60 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-28 02:09:39,337] [pool-1-thread-1] Initializing /data/public/eliana/retina_large.ims: [testng] 02:09:39,337 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:09:39,337 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:39,339 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-28_02-09-39.log] [testng] 02:09:39,339 |-INFO in ch.qos.logback.core.sift.SiftProcessor@429e4627 - End of configuration. [testng] [2024-07-28 02:09:39,395] [pool-1-thread-12] Initializing /data/gh-4193/24-5-9_RSV+AfumMscar+CFW_40x Stack_deconvolved.ims: [testng] 02:09:39,395 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:09:39,395 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:39,396 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-28_02-09-39.log] [testng] 02:09:39,397 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65146a09 - End of configuration. [testng] [2024-07-28 02:09:39,501] [pool-1-thread-11] Initializing /data/public/davemason/Convallaria_3C_3T_2x2grid_confocal.ims: [testng] 02:09:39,501 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:09:39,501 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:39,502 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-28_02-09-39.log] [testng] 02:09:39,502 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7380a7bd - End of configuration. [testng] [2024-07-28 02:09:39,547] [pool-1-thread-10] Initializing /data/kay/Imaris503_test_Kay.ims: [testng] 02:09:39,548 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:09:39,548 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:39,549 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-28_02-09-39.log] [testng] 02:09:39,549 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f013f63 - End of configuration. [testng] [2024-07-28 02:09:39,580] [pool-1-thread-9] Initializing /data/public/davemason/Convallaria_3C_3T_35Z_confocal_deconvolved_IMS3.ims: [testng] 02:09:39,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:09:39,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:39,582 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-28_02-09-39.log] [testng] 02:09:39,583 |-INFO in ch.qos.logback.core.sift.SiftProcessor@bec769e - End of configuration. [testng] [2024-07-28 02:09:39,639] [pool-1-thread-8] Initializing /data/generated/10-31_E_t0006.ims: [testng] 02:09:39,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:09:39,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:39,641 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-28_02-09-39.log] [testng] 02:09:39,641 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ec60f33 - End of configuration. [testng] [2024-07-28 02:09:39,661] [pool-1-thread-7] Initializing /data/oliver/Stack2_u16Bit.ims: [testng] 02:09:39,661 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:09:39,661 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:39,662 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-28_02-09-39.log] [testng] 02:09:39,663 |-INFO in ch.qos.logback.core.sift.SiftProcessor@295b69ee - End of configuration. [testng] [2024-07-28 02:09:39,703] [pool-1-thread-6] Initializing /data/generated/10-31_E_t0013.ims: [testng] 02:09:39,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:09:39,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:39,705 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-28_02-09-39.log] [testng] 02:09:39,706 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d00453d - End of configuration. [testng] [2024-07-28 02:09:39,723] [pool-1-thread-5] Initializing /data/jason/imaris_5_5_demoimages/HeLaCell.ims: [testng] 02:09:39,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:09:39,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:39,724 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-28_02-09-39.log] [testng] 02:09:39,724 |-INFO in ch.qos.logback.core.sift.SiftProcessor@446d7791 - End of configuration. [testng] [2024-07-28 02:09:39,761] [pool-1-thread-4] Initializing /data/qa-8019/wrong_num_dimensions.ims: [testng] 02:09:39,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:09:39,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:39,762 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-28_02-09-39.log] [testng] 02:09:39,763 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f8319de - End of configuration. [testng] [2024-07-28 02:09:39,826] [pool-1-thread-3] Initializing /data/jason/imaris_5_5_demoimages/SwimmingAlgae.ims: [testng] 02:09:39,826 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:09:39,826 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:39,828 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-28_02-09-39.log] [testng] 02:09:39,828 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ac141d4 - End of configuration. [testng] [2024-07-28 02:09:39,884] [pool-1-thread-2] Initializing /data/public/davemason/Convallaria_3C_1T_2x2grid_confocal.ims: [testng] 02:09:39,884 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:09:39,884 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:09:39,885 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-28_02-09-39.log] [testng] 02:09:39,886 |-INFO in ch.qos.logback.core.sift.SiftProcessor@420c5225 - End of configuration. BUILD SUCCESSFUL Total time: 1 minute 41 seconds Finished: SUCCESS