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Started by upstream project "BIOFORMATS-test-repo" build number 109 originally caused by: Started by upstream project "Trigger" build number 122 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins15667512437397694367.sh + '[' analyze = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_16978_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] 12:57:44,208 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 12:57:44,210 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 12:57:44,210 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:57:44,211 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:57:44,211 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 12:57:44,212 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 12:57:44,212 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 12:57:44,212 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:57:44,212 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:57:44,213 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 12:57:44,213 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 12:57:44,214 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 12:57:44,387 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 12:57:44,387 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 12:57:44,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 12:57:44,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 12:57:44,440 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 12:57:44,441 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 12:57:44,441 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 12:57:44,442 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 12:57:44,442 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 12:57:44,443 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 12:57:44,444 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 232 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-02 12:57:44,463] [main] java.version = 11.0.16 [testng] 12:57:44,467 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 12:57:44,467 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:57:44,520 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-02_12-57-44.log] [testng] 12:57:44,522 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-07-02 12:57:44,524] [main] testng.directory = /data [testng] [2024-07-02 12:57:44,524] [main] testng.configDirectory = /config [testng] [2024-07-02 12:57:44,535] [main] testng.multiplier = 1.0 [testng] [2024-07-02 12:57:44,536] [main] testng.in-memory = false [testng] [2024-07-02 12:57:44,536] [main] testng.allow-missing = false [testng] [2024-07-02 12:57:44,537] [main] user.language = en [testng] [2024-07-02 12:57:44,537] [main] user.country = ${user.country} [testng] [2024-07-02 12:57:44,537] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-02 12:57:45,205] [main] ---------------------------------------- [testng] [2024-07-02 12:57:45,205] [main] Total files: 21 [testng] [2024-07-02 12:57:45,205] [main] Scan time: 0.668 s (31 ms/file) [testng] [2024-07-02 12:57:45,205] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-02 12:57:48,164] [pool-1-thread-1] Initializing /data/frans/Test Files for Frans/1002-sag-transform-box-est_flip-ord.hdr: [testng] 12:57:48,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 12:57:48,166 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:57:48,168 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-02_12-57-48.log] [testng] 12:57:48,168 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4aa71d64 - End of configuration. [testng] [2024-07-02 12:57:48,290] [pool-1-thread-12] Initializing /data/frans/Test Files for Frans/F005_1002_MF_SCAN1_stat_brain_fdg_JJ_Volume_Corrected.hdr: [testng] 12:57:48,291 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 12:57:48,291 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:57:48,293 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-02_12-57-48.log] [testng] 12:57:48,294 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e2aca05 - End of configuration. [testng] [2024-07-02 12:57:48,313] [pool-1-thread-11] Initializing /data/frans/CT_FOOT.hdr: [testng] 12:57:48,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 12:57:48,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:57:48,315 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-02_12-57-48.log] [testng] 12:57:48,316 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7678e2e7 - End of configuration. [testng] [2024-07-02 12:57:48,332] [pool-1-thread-10] Initializing /data/frans/CT_WHOLE.hdr: [testng] 12:57:48,332 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 12:57:48,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:57:48,333 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-02_12-57-48.log] [testng] 12:57:48,334 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7eaffbc4 - End of configuration. [testng] [2024-07-02 12:57:48,346] [pool-1-thread-9] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1.img.hdr: [testng] 12:57:48,347 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 12:57:48,347 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:57:48,347 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-02_12-57-48.log] [testng] 12:57:48,348 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36980d38 - End of configuration. [testng] [2024-07-02 12:57:48,361] [pool-1-thread-8] Initializing /data/frans/MR_CHEST.hdr: [testng] 12:57:48,362 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 12:57:48,362 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:57:48,363 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-02_12-57-48.log] [testng] 12:57:48,363 |-INFO in ch.qos.logback.core.sift.SiftProcessor@281b0875 - End of configuration. [testng] [2024-07-02 12:57:48,378] [pool-1-thread-7] Initializing /data/frans/ch2.hdr: [testng] 12:57:48,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 12:57:48,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:57:48,379 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-02_12-57-48.log] [testng] 12:57:48,379 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21425844 - End of configuration. [testng] [2024-07-02 12:57:48,396] [pool-1-thread-6] Initializing /data/frans/betmask.hdr: [testng] 12:57:48,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 12:57:48,396 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:57:48,397 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-02_12-57-48.log] [testng] 12:57:48,397 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72abc591 - End of configuration. [testng] [2024-07-02 12:57:48,408] [pool-1-thread-5] Initializing /data/frans/aal.hdr: [testng] 12:57:48,409 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 12:57:48,409 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:57:48,409 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-02_12-57-48.log] [testng] 12:57:48,410 |-INFO in ch.qos.logback.core.sift.SiftProcessor@cb0832c - End of configuration. [testng] [2024-07-02 12:57:48,423] [pool-1-thread-4] Initializing /data/frans/Test Files for Frans/200-PLA_sansBD_spmT_0005.hdr: [testng] 12:57:48,424 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 12:57:48,424 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:57:48,424 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-02_12-57-48.log] [testng] 12:57:48,425 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69deadbb - End of configuration. [testng] [2024-07-02 12:57:48,435] [pool-1-thread-3] Initializing /data/frans/ch2bet.hdr: [testng] 12:57:48,436 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 12:57:48,436 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:57:48,436 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-02_12-57-48.log] [testng] 12:57:48,437 |-INFO in ch.qos.logback.core.sift.SiftProcessor@508c8310 - End of configuration. [testng] [2024-07-02 12:57:48,447] [pool-1-thread-2] Initializing /data/frans/CT_KNEE.hdr: [testng] 12:57:48,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 12:57:48,447 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:57:48,448 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-02_12-57-48.log] [testng] 12:57:48,448 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e52192e - End of configuration. [testng] [2024-07-02 12:57:50,048] [pool-1-thread-4] Initializing /data/frans/CT_CRANI.hdr: [testng] [2024-07-02 12:57:50,061] [pool-1-thread-6] Initializing /data/frans/brodmann.hdr: [testng] [2024-07-02 12:57:50,070] [pool-1-thread-12] Initializing /data/frans/Test Files for Frans/PLA-zm2-16mm_1002_MF_V1.hdr: [testng] [2024-07-02 12:57:50,081] [pool-1-thread-9] Initializing /data/frans/MR_SEGBRAIN.hdr: [testng] [2024-07-02 12:57:50,332] [pool-1-thread-7] Initializing /data/frans/CT_APERT.hdr: [testng] [2024-07-02 12:57:50,341] [pool-1-thread-8] Initializing /data/frans/CT_HAND.hdr: [testng] [2024-07-02 12:57:50,351] [pool-1-thread-5] Initializing /data/frans/CT_CHEST.hdr: [testng] [2024-07-02 12:57:50,363] [pool-1-thread-1] Initializing /data/frans/Test Files for Frans/06-101-mask-40pc2dil.hdr: [testng] [2024-07-02 12:57:50,374] [pool-1-thread-10] 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: 9 seconds Finished: SUCCESS