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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@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins4496439916720334784.sh + '[' nifti = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_17014_merge_ci -v /uod/idr/repos/curated/nifti:/data -v /uod/idr-scratch/merge-ci/curated/nifti:/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] 13:22:15,071 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 13:22:15,073 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 13:22:15,073 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 13:22:15,074 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 13:22:15,074 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 13:22:15,075 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 13:22:15,075 |-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] 13:22:15,075 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 13:22:15,076 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 13:22:15,076 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 13:22:15,077 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 13:22:15,077 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 13:22:15,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 13:22:15,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 13:22:15,260 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 13:22:15,260 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 13:22:15,266 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 13:22:15,266 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 13:22:15,266 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 13:22:15,267 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 13:22:15,267 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 13:22:15,268 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 13:22:15,268 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 192 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-02 13:22:15,278] [main] java.version = 11.0.16 [testng] 13:22:15,281 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 13:22:15,281 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:22:15,323 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-02_13-22-15.log] [testng] 13:22:15,324 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-07-02 13:22:15,326] [main] testng.directory = /data [testng] [2024-07-02 13:22:15,327] [main] testng.configDirectory = /config [testng] [2024-07-02 13:22:15,336] [main] testng.multiplier = 1.0 [testng] [2024-07-02 13:22:15,337] [main] testng.in-memory = false [testng] [2024-07-02 13:22:15,337] [main] testng.allow-missing = false [testng] [2024-07-02 13:22:15,337] [main] user.language = en [testng] [2024-07-02 13:22:15,337] [main] user.country = ${user.country} [testng] [2024-07-02 13:22:15,337] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-02 13:22:16,090] [main] ---------------------------------------- [testng] [2024-07-02 13:22:16,090] [main] Total files: 23 [testng] [2024-07-02 13:22:16,090] [main] Scan time: 0.753 s (32 ms/file) [testng] [2024-07-02 13:22:16,090] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-02 13:22:20,374] [pool-1-thread-1] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_26_conf_91.hdr: [testng] 13:22:20,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 13:22:20,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:22:20,376 |-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_13-22-20.log] [testng] 13:22:20,377 |-INFO in ch.qos.logback.core.sift.SiftProcessor@389a6c66 - End of configuration. [testng] [2024-07-02 13:22:20,397] [pool-1-thread-12] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_94.hdr: [testng] 13:22:20,397 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 13:22:20,397 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:22:20,398 |-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_13-22-20.log] [testng] 13:22:20,399 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2450c3a2 - End of configuration. [testng] [2024-07-02 13:22:20,412] [pool-1-thread-11] Initializing /data/qa-17334/volume4d.nii: [testng] 13:22:20,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 13:22:20,412 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:22:20,413 |-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_13-22-20.log] [testng] 13:22:20,413 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60dfd808 - End of configuration. [testng] [2024-07-02 13:22:20,436] [pool-1-thread-10] Initializing /data/public/NIH/newsirp_final_XML.nii: [testng] 13:22:20,436 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 13:22:20,436 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:22:20,437 |-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_13-22-20.log] [testng] 13:22:20,438 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6854e89b - End of configuration. [testng] [2024-07-02 13:22:20,465] [pool-1-thread-9] Initializing /data/public/NIH/avg152T1_LR_nifti.nii.gz: [testng] 13:22:20,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 13:22:20,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:22:20,466 |-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_13-22-20.log] [testng] 13:22:20,467 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d550f00 - End of configuration. [testng] [2024-07-02 13:22:20,639] [pool-1-thread-8] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_100.hdr: [testng] 13:22:20,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 13:22:20,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:22:20,640 |-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_13-22-20.log] [testng] 13:22:20,640 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e8da041 - End of configuration. [testng] [2024-07-02 13:22:20,653] [pool-1-thread-7] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_27_conf_86.hdr: [testng] 13:22:20,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 13:22:20,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:22:20,654 |-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_13-22-20.log] [testng] 13:22:20,654 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a9d771a - End of configuration. [testng] [2024-07-02 13:22:20,665] [pool-1-thread-6] Initializing /data/public/NIH/avg152T1_RL_nifti.nii.gz: [testng] 13:22:20,665 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 13:22:20,665 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:22:20,666 |-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_13-22-20.log] [testng] 13:22:20,666 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37081102 - End of configuration. [testng] [2024-07-02 13:22:20,839] [pool-1-thread-5] Initializing /data/public/NIH/minimal.hdr: [testng] 13:22:20,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 13:22:20,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:22:20,840 |-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_13-22-20.log] [testng] 13:22:20,840 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37370e56 - End of configuration. [testng] [2024-07-02 13:22:20,850] [pool-1-thread-4] Initializing /data/public/NIH/avg152T1_RL_nifti.nii: [testng] 13:22:20,851 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 13:22:20,851 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:22:20,852 |-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_13-22-20.log] [testng] 13:22:20,852 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43d6a3b1 - End of configuration. [testng] [2024-07-02 13:22:20,872] [pool-1-thread-3] Initializing /data/public/NIH/avg152T1_LR_nifti.nii: [testng] 13:22:20,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 13:22:20,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:22:20,873 |-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_13-22-20.log] [testng] 13:22:20,873 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26d80166 - End of configuration. [testng] [2024-07-02 13:22:20,899] [pool-1-thread-2] Initializing /data/public/NIH/zstat1.nii: [testng] 13:22:20,899 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 13:22:20,899 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:22:20,900 |-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_13-22-20.log] [testng] 13:22:20,900 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a120c9f - End of configuration. [testng] [2024-07-02 13:22:22,342] [pool-1-thread-5] Initializing /data/public/NIH/avg152T1_LR_nifti.hdr: [testng] [2024-07-02 13:22:22,353] [pool-1-thread-2] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_100.hdr: [testng] [2024-07-02 13:22:22,364] [pool-1-thread-11] Initializing /data/public/NIH/minimal.nii: [testng] [2024-07-02 13:22:22,374] [pool-1-thread-1] Initializing /data/public/NIH/avg152T1_RL_nifti.hdr: [testng] [2024-07-02 13:22:22,387] [pool-1-thread-8] Initializing /data/public/NIH/zstat1.nii.gz: [testng] [2024-07-02 13:22:22,462] [pool-1-thread-12] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_94.hdr: [testng] [2024-07-02 13:22:22,471] [pool-1-thread-7] Initializing /data/public/NIH/filtered_func_data.nii: [testng] [2024-07-02 13:22:22,486] [pool-1-thread-10] Initializing /data/public/NIH/filtered_func_data.nii.gz: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1060, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 38 seconds Finished: SUCCESS