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Started by upstream project "BIOFORMATS-test-repo" build number 116 originally caused by: Started by upstream project "Trigger" build number 133 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins9239140584665617317.sh + '[' analyze = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_18126_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] 02:10:46,335 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:10:46,336 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 02:10:46,336 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:10:46,337 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:10:46,338 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:10:46,338 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:10:46,338 |-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] 02:10:46,338 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:10:46,339 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:10:46,339 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:10:46,339 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:10:46,340 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:10:46,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:10:46,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:10:46,520 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:10:46,520 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:10:46,525 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:10:46,526 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:10:46,526 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:10:46,526 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:10:46,526 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 02:10:46,527 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 02:10:46,527 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 188 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-10 02:10:46,536] [main] java.version = 17.0.2 [testng] 02:10:46,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:10:46,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:46,578 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-10_02-10-46.log] [testng] 02:10:46,579 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-07-10 02:10:46,581] [main] testng.directory = /data [testng] [2024-07-10 02:10:46,581] [main] testng.configDirectory = /config [testng] [2024-07-10 02:10:46,589] [main] testng.multiplier = 1.0 [testng] [2024-07-10 02:10:46,590] [main] testng.in-memory = false [testng] [2024-07-10 02:10:46,590] [main] testng.allow-missing = false [testng] [2024-07-10 02:10:46,590] [main] user.language = en [testng] [2024-07-10 02:10:46,590] [main] user.country = ${user.country} [testng] [2024-07-10 02:10:46,590] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-10 02:10:47,192] [main] ---------------------------------------- [testng] [2024-07-10 02:10:47,192] [main] Total files: 21 [testng] [2024-07-10 02:10:47,192] [main] Scan time: 0.601 s (28 ms/file) [testng] [2024-07-10 02:10:47,192] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-10 02:10:48,482] [pool-1-thread-1] Initializing /data/frans/Test Files for Frans/1002-sag-transform-box-est_flip-ord.hdr: [testng] 02:10:48,482 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:10:48,482 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:48,483 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-10_02-10-48.log] [testng] 02:10:48,484 |-INFO in ch.qos.logback.core.sift.SiftProcessor@341feadd - End of configuration. [testng] [2024-07-10 02:10:48,539] [pool-1-thread-12] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1.img.hdr: [testng] 02:10:48,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:10:48,539 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:48,540 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-10_02-10-48.log] [testng] 02:10:48,541 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5243f734 - End of configuration. [testng] [2024-07-10 02:10:48,553] [pool-1-thread-11] Initializing /data/frans/Test Files for Frans/200-PLA_sansBD_spmT_0005.hdr: [testng] 02:10:48,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:10:48,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:48,555 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-10_02-10-48.log] [testng] 02:10:48,555 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ae53be5 - End of configuration. [testng] [2024-07-10 02:10:48,568] [pool-1-thread-10] Initializing /data/frans/Test Files for Frans/06-101-mask-40pc2dil.hdr: [testng] 02:10:48,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:10:48,568 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:48,569 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-10_02-10-48.log] [testng] 02:10:48,570 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4288c468 - End of configuration. [testng] [2024-07-10 02:10:48,583] [pool-1-thread-9] Initializing /data/frans/Test Files for Frans/F005_1002_MF_SCAN1_stat_brain_fdg_JJ_Volume_Corrected.hdr: [testng] 02:10:48,583 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:10:48,583 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:48,584 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-10_02-10-48.log] [testng] 02:10:48,584 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2082a6ed - End of configuration. [testng] [2024-07-10 02:10:48,597] [pool-1-thread-8] Initializing /data/frans/ch2bet.hdr: [testng] 02:10:48,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:10:48,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:48,599 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-10_02-10-48.log] [testng] 02:10:48,599 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60ba4c2a - End of configuration. [testng] [2024-07-10 02:10:48,612] [pool-1-thread-7] Initializing /data/frans/brodmann.hdr: [testng] 02:10:48,612 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:10:48,612 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:48,613 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-10_02-10-48.log] [testng] 02:10:48,613 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d51f4c3 - End of configuration. [testng] [2024-07-10 02:10:48,625] [pool-1-thread-6] Initializing /data/frans/CT_FOOT.hdr: [testng] 02:10:48,625 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:10:48,625 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:48,626 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-10_02-10-48.log] [testng] 02:10:48,626 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71390107 - End of configuration. [testng] [2024-07-10 02:10:48,637] [pool-1-thread-5] Initializing /data/frans/CT_CRANI.hdr: [testng] 02:10:48,638 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:10:48,638 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:48,638 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-10_02-10-48.log] [testng] 02:10:48,639 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25d4b6f0 - End of configuration. [testng] [2024-07-10 02:10:48,650] [pool-1-thread-4] Initializing /data/frans/betmask.hdr: [testng] 02:10:48,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:10:48,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:48,651 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-10_02-10-48.log] [testng] 02:10:48,651 |-INFO in ch.qos.logback.core.sift.SiftProcessor@523cbb1b - End of configuration. [testng] [2024-07-10 02:10:48,661] [pool-1-thread-3] Initializing /data/frans/m000-MR_CHEST.gif: [testng] 02:10:48,661 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:10:48,661 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:48,662 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-10_02-10-48.log] [testng] 02:10:48,662 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2cb74f7e - End of configuration. [testng] [2024-07-10 02:10:48,685] [pool-1-thread-2] Initializing /data/frans/Test Files for Frans/PLA-zm2-16mm_1002_MF_V1.hdr: [testng] 02:10:48,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:10:48,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:48,686 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-10_02-10-48.log] [testng] 02:10:48,686 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3cbe01c8 - End of configuration. [testng] [2024-07-10 02:10:50,224] [pool-1-thread-4] Initializing /data/frans/CT_APERT.hdr: [testng] [2024-07-10 02:10:50,234] [pool-1-thread-9] Initializing /data/frans/CT_HAND.hdr: [testng] [2024-07-10 02:10:50,245] [pool-1-thread-12] Initializing /data/frans/ch2.hdr: [testng] [2024-07-10 02:10:50,257] [pool-1-thread-5] Initializing /data/frans/aal.hdr: [testng] [2024-07-10 02:10:50,267] [pool-1-thread-8] Initializing /data/frans/MR_CHEST.hdr: [testng] [2024-07-10 02:10:50,277] [pool-1-thread-7] Initializing /data/frans/CT_CHEST.hdr: [testng] [2024-07-10 02:10:50,288] [pool-1-thread-1] Initializing /data/frans/CT_WHOLE.hdr: [testng] [2024-07-10 02:10:50,301] [pool-1-thread-3] Initializing /data/frans/MR_SEGBRAIN.hdr: [testng] [2024-07-10 02:10:50,313] [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