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Started by upstream project "BIOFORMATS-test-repo" build number 126 originally caused by: Started by upstream project "Trigger" build number 143 originally caused by: Started by timer 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/jenkins1518470673961635858.sh + '[' analyze = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_19766_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] 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] 02:13:14,085 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:13:14,088 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 02:13:14,088 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:13:14,090 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:13:14,091 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:13:14,092 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:13:14,092 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:13:14,092 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:13:14,093 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:13:14,095 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:13:14,095 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:13:14,096 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:13:14,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:13:14,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:13:14,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:13:14,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:13:14,366 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:13:14,367 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:13:14,367 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:13:14,367 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:13:14,367 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 02:13:14,368 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 02:13:14,369 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 276 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-20 02:13:14,379] [main] java.version = 11.0.16 [testng] 02:13:14,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:13:14,383 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:14,432 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-20_02-13-14.log] [testng] 02:13:14,433 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-07-20 02:13:14,436] [main] testng.directory = /data [testng] [2024-07-20 02:13:14,436] [main] testng.configDirectory = /config [testng] [2024-07-20 02:13:14,448] [main] testng.multiplier = 1.0 [testng] [2024-07-20 02:13:14,449] [main] testng.in-memory = false [testng] [2024-07-20 02:13:14,449] [main] testng.allow-missing = false [testng] [2024-07-20 02:13:14,449] [main] user.language = en [testng] [2024-07-20 02:13:14,449] [main] user.country = ${user.country} [testng] [2024-07-20 02:13:14,450] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-20 02:13:15,185] [main] ---------------------------------------- [testng] [2024-07-20 02:13:15,185] [main] Total files: 21 [testng] [2024-07-20 02:13:15,185] [main] Scan time: 0.735 s (35 ms/file) [testng] [2024-07-20 02:13:15,186] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-20 02:13:17,430] [pool-1-thread-1] Initializing /data/frans/Test Files for Frans/1002-sag-transform-box-est_flip-ord.hdr: [testng] 02:13:17,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:13:17,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:17,434 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-20_02-13-17.log] [testng] 02:13:17,435 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68bc1c72 - End of configuration. [testng] [2024-07-20 02:13:17,496] [pool-1-thread-12] Initializing /data/frans/Test Files for Frans/F005_1002_MF_SCAN1_stat_brain_fdg_JJ_Volume_Corrected.hdr: [testng] 02:13:17,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:13:17,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:17,498 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-20_02-13-17.log] [testng] 02:13:17,498 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43338b56 - End of configuration. [testng] [2024-07-20 02:13:17,514] [pool-1-thread-11] Initializing /data/frans/CT_FOOT.hdr: [testng] 02:13:17,514 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:13:17,514 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:17,515 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-20_02-13-17.log] [testng] 02:13:17,516 |-INFO in ch.qos.logback.core.sift.SiftProcessor@635f2c8 - End of configuration. [testng] [2024-07-20 02:13:17,532] [pool-1-thread-10] Initializing /data/frans/CT_WHOLE.hdr: [testng] 02:13:17,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:13:17,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:17,534 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-20_02-13-17.log] [testng] 02:13:17,535 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a65a3ac - End of configuration. [testng] [2024-07-20 02:13:17,556] [pool-1-thread-9] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1.img.hdr: [testng] 02:13:17,557 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:13:17,557 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:17,558 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-20_02-13-17.log] [testng] 02:13:17,558 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51dd021f - End of configuration. [testng] [2024-07-20 02:13:17,577] [pool-1-thread-8] Initializing /data/frans/MR_CHEST.hdr: [testng] 02:13:17,577 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:13:17,577 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:17,578 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-20_02-13-17.log] [testng] 02:13:17,578 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5718fb8c - End of configuration. [testng] [2024-07-20 02:13:17,592] [pool-1-thread-7] Initializing /data/frans/ch2.hdr: [testng] 02:13:17,592 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:13:17,592 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:17,593 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-20_02-13-17.log] [testng] 02:13:17,593 |-INFO in ch.qos.logback.core.sift.SiftProcessor@74e9ae49 - End of configuration. [testng] [2024-07-20 02:13:17,606] [pool-1-thread-6] Initializing /data/frans/betmask.hdr: [testng] 02:13:17,607 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:13:17,607 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:17,608 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-20_02-13-17.log] [testng] 02:13:17,608 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11640507 - End of configuration. [testng] [2024-07-20 02:13:17,624] [pool-1-thread-5] Initializing /data/frans/aal.hdr: [testng] 02:13:17,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:13:17,624 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:17,625 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-20_02-13-17.log] [testng] 02:13:17,625 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2519641b - End of configuration. [testng] [2024-07-20 02:13:17,642] [pool-1-thread-4] Initializing /data/frans/Test Files for Frans/200-PLA_sansBD_spmT_0005.hdr: [testng] 02:13:17,642 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:13:17,642 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:17,642 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-20_02-13-17.log] [testng] 02:13:17,643 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3758dde7 - End of configuration. [testng] [2024-07-20 02:13:17,659] [pool-1-thread-3] Initializing /data/frans/ch2bet.hdr: [testng] 02:13:17,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:13:17,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:17,660 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-20_02-13-17.log] [testng] 02:13:17,661 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a651a84 - End of configuration. [testng] [2024-07-20 02:13:17,676] [pool-1-thread-2] Initializing /data/frans/CT_KNEE.hdr: [testng] 02:13:17,676 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:13:17,676 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:13:17,677 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-20_02-13-17.log] [testng] 02:13:17,678 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45a1fabb - End of configuration. [testng] [2024-07-20 02:13:19,358] [pool-1-thread-4] Initializing /data/frans/CT_CRANI.hdr: [testng] [2024-07-20 02:13:19,383] [pool-1-thread-12] Initializing /data/frans/brodmann.hdr: [testng] [2024-07-20 02:13:19,400] [pool-1-thread-9] Initializing /data/frans/Test Files for Frans/PLA-zm2-16mm_1002_MF_V1.hdr: [testng] [2024-07-20 02:13:19,419] [pool-1-thread-6] Initializing /data/frans/MR_SEGBRAIN.hdr: [testng] [2024-07-20 02:13:20,044] [pool-1-thread-8] Initializing /data/frans/CT_APERT.hdr: [testng] [2024-07-20 02:13:20,055] [pool-1-thread-10] Initializing /data/frans/CT_HAND.hdr: [testng] [2024-07-20 02:13:20,070] [pool-1-thread-7] Initializing /data/frans/CT_CHEST.hdr: [testng] [2024-07-20 02:13:20,089] [pool-1-thread-11] Initializing /data/frans/Test Files for Frans/06-101-mask-40pc2dil.hdr: [testng] [2024-07-20 02:13:20,113] [pool-1-thread-1] Initializing /data/frans/m000-MR_CHEST.gif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1113, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 10 seconds Finished: SUCCESS