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Started by upstream project "BIOFORMATS-test-repo" build number 123 originally caused by: Started by upstream project "Trigger" build number 140 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins8892649934990881813.sh + '[' analyze = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_19274_merge_ci -v /uod/idr/repos/curated/analyze:/data -v /uod/idr-scratch/merge-ci/curated/analyze:/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] 02:10:48,047 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:10:48,048 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 02:10:48,048 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:10:48,049 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:10:48,049 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:10:48,050 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:10:48,050 |-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] 02:10:48,050 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:10:48,051 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:10:48,051 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:10:48,051 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:10:48,052 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:10:48,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:10:48,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:10:48,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:10:48,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:10:48,245 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:10:48,245 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:10:48,245 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:10:48,245 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:10:48,245 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 02:10:48,246 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 02:10:48,246 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 195 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-17 02:10:48,255] [main] java.version = 17.0.2 [testng] 02:10:48,258 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:10:48,258 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:48,299 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-17_02-10-48.log] [testng] 02:10:48,301 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-07-17 02:10:48,303] [main] testng.directory = /data [testng] [2024-07-17 02:10:48,303] [main] testng.configDirectory = /config [testng] [2024-07-17 02:10:48,311] [main] testng.multiplier = 1.0 [testng] [2024-07-17 02:10:48,312] [main] testng.in-memory = false [testng] [2024-07-17 02:10:48,312] [main] testng.allow-missing = false [testng] [2024-07-17 02:10:48,312] [main] user.language = en [testng] [2024-07-17 02:10:48,312] [main] user.country = ${user.country} [testng] [2024-07-17 02:10:48,312] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-17 02:10:48,873] [main] ---------------------------------------- [testng] [2024-07-17 02:10:48,873] [main] Total files: 21 [testng] [2024-07-17 02:10:48,873] [main] Scan time: 0.561 s (26 ms/file) [testng] [2024-07-17 02:10:48,873] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-17 02:10:50,671] [pool-1-thread-1] Initializing /data/frans/Test Files for Frans/1002-sag-transform-box-est_flip-ord.hdr: [testng] 02:10:50,672 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:10:50,672 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:50,673 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-17_02-10-50.log] [testng] 02:10:50,673 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b858dd3 - End of configuration. [testng] [2024-07-17 02:10:50,731] [pool-1-thread-12] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1.img.hdr: [testng] 02:10:50,731 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:10:50,731 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:50,732 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-17_02-10-50.log] [testng] 02:10:50,733 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ebe0817 - End of configuration. [testng] [2024-07-17 02:10:50,748] [pool-1-thread-11] Initializing /data/frans/Test Files for Frans/200-PLA_sansBD_spmT_0005.hdr: [testng] 02:10:50,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:10:50,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:50,749 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-17_02-10-50.log] [testng] 02:10:50,750 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78014c69 - End of configuration. [testng] [2024-07-17 02:10:50,763] [pool-1-thread-10] Initializing /data/frans/Test Files for Frans/06-101-mask-40pc2dil.hdr: [testng] 02:10:50,763 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:10:50,763 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:50,764 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-17_02-10-50.log] [testng] 02:10:50,764 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a38dfd9 - End of configuration. [testng] [2024-07-17 02:10:50,777] [pool-1-thread-9] Initializing /data/frans/Test Files for Frans/F005_1002_MF_SCAN1_stat_brain_fdg_JJ_Volume_Corrected.hdr: [testng] 02:10:50,777 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:10:50,777 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:50,778 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-17_02-10-50.log] [testng] 02:10:50,778 |-INFO in ch.qos.logback.core.sift.SiftProcessor@189732ca - End of configuration. [testng] [2024-07-17 02:10:50,792] [pool-1-thread-8] Initializing /data/frans/ch2bet.hdr: [testng] 02:10:50,792 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:10:50,793 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:50,793 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-17_02-10-50.log] [testng] 02:10:50,794 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75aa376e - End of configuration. [testng] [2024-07-17 02:10:50,815] [pool-1-thread-7] Initializing /data/frans/brodmann.hdr: [testng] 02:10:50,815 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:10:50,815 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:50,817 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-17_02-10-50.log] [testng] 02:10:50,817 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39103b8a - End of configuration. [testng] [2024-07-17 02:10:50,832] [pool-1-thread-6] Initializing /data/frans/CT_FOOT.hdr: [testng] 02:10:50,832 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:10:50,832 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:50,833 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-17_02-10-50.log] [testng] 02:10:50,834 |-INFO in ch.qos.logback.core.sift.SiftProcessor@cac88ed - End of configuration. [testng] [2024-07-17 02:10:50,847] [pool-1-thread-5] Initializing /data/frans/CT_CRANI.hdr: [testng] 02:10:50,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:10:50,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:50,848 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-17_02-10-50.log] [testng] 02:10:50,848 |-INFO in ch.qos.logback.core.sift.SiftProcessor@339e99d1 - End of configuration. [testng] [2024-07-17 02:10:50,860] [pool-1-thread-4] Initializing /data/frans/betmask.hdr: [testng] 02:10:50,860 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:10:50,860 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:50,861 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-17_02-10-50.log] [testng] 02:10:50,861 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27c0fc43 - End of configuration. [testng] [2024-07-17 02:10:50,870] [pool-1-thread-3] Initializing /data/frans/m000-MR_CHEST.gif: [testng] 02:10:50,871 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:10:50,871 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:50,872 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-17_02-10-50.log] [testng] 02:10:50,872 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23486705 - End of configuration. [testng] [2024-07-17 02:10:50,894] [pool-1-thread-2] Initializing /data/frans/Test Files for Frans/PLA-zm2-16mm_1002_MF_V1.hdr: [testng] 02:10:50,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:10:50,895 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:50,895 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-17_02-10-50.log] [testng] 02:10:50,896 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7418af50 - End of configuration. [testng] [2024-07-17 02:10:52,459] [pool-1-thread-10] Initializing /data/frans/CT_APERT.hdr: [testng] [2024-07-17 02:10:52,470] [pool-1-thread-12] Initializing /data/frans/CT_HAND.hdr: [testng] [2024-07-17 02:10:52,483] [pool-1-thread-2] Initializing /data/frans/ch2.hdr: [testng] [2024-07-17 02:10:52,493] [pool-1-thread-1] Initializing /data/frans/aal.hdr: [testng] [2024-07-17 02:10:52,503] [pool-1-thread-3] Initializing /data/frans/MR_CHEST.hdr: [testng] [2024-07-17 02:10:52,512] [pool-1-thread-5] Initializing /data/frans/CT_CHEST.hdr: [testng] [2024-07-17 02:10:52,523] [pool-1-thread-7] Initializing /data/frans/CT_WHOLE.hdr: [testng] [2024-07-17 02:10:52,533] [pool-1-thread-8] Initializing /data/frans/MR_SEGBRAIN.hdr: [testng] [2024-07-17 02:10:52,541] [pool-1-thread-6] Initializing /data/frans/CT_KNEE.hdr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1113, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 9 seconds Finished: SUCCESS