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Started by upstream project "BIOFORMATS-test-repo" build number 243 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@10 [BIOFORMATS-test-folder@10] $ /bin/bash -xe /tmp/jenkins5672125278535878155.sh + '[' nifti = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_38317_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] 17:24:20,746 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 17:24:20,748 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 17:24:20,748 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 17:24:20,749 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 17:24:20,749 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 17:24:20,749 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 17:24:20,750 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 17:24:20,750 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 17:24:20,750 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 17:24:20,751 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 17:24:20,751 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 17:24:20,751 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 17:24:20,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 17:24:20,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 17:24:20,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 17:24:20,929 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 17:24:20,934 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 17:24:20,934 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 17:24:20,934 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 17:24:20,934 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 17:24:20,934 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 17:24:20,935 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 17:24:20,935 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 185 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-02 17:24:20,943] [main] java.version = 11.0.16 [testng] 17:24:20,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 17:24:20,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:24:20,986 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-02_17-24-20.log] [testng] 17:24:20,988 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-11-02 17:24:20,989] [main] testng.directory = /data [testng] [2024-11-02 17:24:20,989] [main] testng.configDirectory = /config [testng] [2024-11-02 17:24:20,998] [main] testng.multiplier = 1.0 [testng] [2024-11-02 17:24:21,000] [main] testng.in-memory = false [testng] [2024-11-02 17:24:21,000] [main] testng.allow-missing = false [testng] [2024-11-02 17:24:21,000] [main] user.language = en [testng] [2024-11-02 17:24:21,000] [main] user.country = ${user.country} [testng] [2024-11-02 17:24:21,000] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-02 17:24:35,494] [main] ---------------------------------------- [testng] [2024-11-02 17:24:35,495] [main] Total files: 23 [testng] [2024-11-02 17:24:35,495] [main] Scan time: 14.494 s (630 ms/file) [testng] [2024-11-02 17:24:35,495] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-02 17:25:10,218] [pool-1-thread-1] Initializing /data/public/NIH/avg152T1_LR_nifti.hdr: [testng] 17:25:10,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 17:25:10,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:25:10,220 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-02_17-25-10.log] [testng] 17:25:10,221 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d90d5ac - End of configuration. [testng] [2024-11-02 17:25:11,239] [pool-1-thread-12] Initializing /data/public/NIH/avg152T1_LR_nifti.nii.gz: [testng] 17:25:11,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 17:25:11,239 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:25:11,240 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-02_17-25-11.log] [testng] 17:25:11,241 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5bdbd907 - End of configuration. [testng] [2024-11-02 17:25:17,530] [pool-1-thread-11] Initializing /data/qa-17334/volume4d.nii: [testng] 17:25:17,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 17:25:17,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:25:17,531 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-02_17-25-17.log] [testng] 17:25:17,531 |-INFO in ch.qos.logback.core.sift.SiftProcessor@15834e9a - End of configuration. [testng] [2024-11-02 17:25:18,528] [pool-1-thread-10] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_94.hdr: [testng] 17:25:18,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 17:25:18,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:25:18,529 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-02_17-25-18.log] [testng] 17:25:18,529 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642dbb8a - End of configuration. [testng] [2024-11-02 17:25:19,519] [pool-1-thread-9] Initializing /data/public/NIH/filtered_func_data.nii: [testng] 17:25:19,520 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 17:25:19,520 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:25:19,520 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-02_17-25-19.log] [testng] 17:25:19,521 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ad4d4c2 - End of configuration. [testng] [2024-11-02 17:25:20,428] [pool-1-thread-8] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_100.hdr: [testng] 17:25:20,428 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 17:25:20,428 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:25:20,429 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-02_17-25-20.log] [testng] 17:25:20,429 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c75ffd7 - End of configuration. [testng] [2024-11-02 17:25:21,481] [pool-1-thread-7] Initializing /data/public/NIH/zstat1.nii.gz: [testng] 17:25:21,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 17:25:21,481 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:25:21,482 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-02_17-25-21.log] [testng] 17:25:21,482 |-INFO in ch.qos.logback.core.sift.SiftProcessor@549c764a - End of configuration. [testng] [2024-11-02 17:25:25,613] [pool-1-thread-6] Initializing /data/public/NIH/avg152T1_RL_nifti.hdr: [testng] 17:25:25,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 17:25:25,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:25:25,614 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-02_17-25-25.log] [testng] 17:25:25,614 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60572624 - End of configuration. [testng] [2024-11-02 17:25:26,650] [pool-1-thread-5] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_27_conf_86.hdr: [testng] 17:25:26,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 17:25:26,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:25:26,651 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-02_17-25-26.log] [testng] 17:25:26,651 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66ffc635 - End of configuration. [testng] [2024-11-02 17:25:27,668] [pool-1-thread-4] Initializing /data/public/NIH/avg152T1_RL_nifti.nii: [testng] 17:25:27,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 17:25:27,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:25:27,669 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-02_17-25-27.log] [testng] 17:25:27,669 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d96c25e - End of configuration. [testng] [2024-11-02 17:25:28,526] [pool-1-thread-3] Initializing /data/public/NIH/newsirp_final_XML.nii: [testng] 17:25:28,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 17:25:28,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:25:28,527 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-02_17-25-28.log] [testng] 17:25:28,527 |-INFO in ch.qos.logback.core.sift.SiftProcessor@cd0fe98 - End of configuration. [testng] [2024-11-02 17:25:29,493] [pool-1-thread-2] Initializing /data/public/NIH/minimal.nii: [testng] 17:25:29,493 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 17:25:29,493 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 17:25:29,494 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-02_17-25-29.log] [testng] 17:25:29,494 |-INFO in ch.qos.logback.core.sift.SiftProcessor@24394eef - End of configuration. [testng] [2024-11-02 17:25:38,031] [pool-1-thread-2] Initializing /data/public/NIH/minimal.hdr: [testng] [2024-11-02 17:25:39,052] [pool-1-thread-4] Initializing /data/public/NIH/avg152T1_LR_nifti.nii: [testng] [2024-11-02 17:25:40,052] [pool-1-thread-11] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_94.hdr: [testng] [2024-11-02 17:25:41,064] [pool-1-thread-9] Initializing /data/public/NIH/avg152T1_RL_nifti.nii.gz: [testng] [2024-11-02 17:25:52,316] [pool-1-thread-3] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_26_conf_91.hdr: [testng] [2024-11-02 17:25:54,797] [pool-1-thread-10] Initializing /data/public/NIH/filtered_func_data.nii.gz: [testng] [2024-11-02 17:26:01,186] [pool-1-thread-6] Initializing /data/public/NIH/zstat1.nii: [testng] [2024-11-02 17:26:03,774] [pool-1-thread-5] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_100.hdr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1060, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 2 minutes 31 seconds Finished: SUCCESS