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Started by upstream project "BIOFORMATS-test-repo" build number 215 originally caused by: Started by upstream project "Trigger" build number 242 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins11562810768932844737.sh + '[' nifti = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_34188_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] 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] 06:15:12,744 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 06:15:12,745 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 06:15:12,745 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:15:12,746 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:15:12,746 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 06:15:12,747 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 06:15:12,747 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 06:15:12,747 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:15:12,747 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:15:12,748 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 06:15:12,748 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 06:15:12,748 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 06:15:12,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 06:15:12,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 06:15:12,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 06:15:12,923 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 06:15:12,928 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 06:15:12,928 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 06:15:12,929 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 06:15:12,929 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 06:15:12,929 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 06:15:12,930 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 06:15:12,930 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 183 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-09 06:15:12,938] [main] java.version = 17.0.2 [testng] 06:15:12,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 06:15:12,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:15:12,980 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-09_06-15-12.log] [testng] 06:15:12,981 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-10-09 06:15:12,983] [main] testng.directory = /data [testng] [2024-10-09 06:15:12,983] [main] testng.configDirectory = /config [testng] [2024-10-09 06:15:12,991] [main] testng.multiplier = 1.0 [testng] [2024-10-09 06:15:12,992] [main] testng.in-memory = false [testng] [2024-10-09 06:15:12,992] [main] testng.allow-missing = false [testng] [2024-10-09 06:15:12,992] [main] user.language = en [testng] [2024-10-09 06:15:12,992] [main] user.country = ${user.country} [testng] [2024-10-09 06:15:12,992] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-09 06:15:36,579] [main] ---------------------------------------- [testng] [2024-10-09 06:15:36,579] [main] Total files: 23 [testng] [2024-10-09 06:15:36,580] [main] Scan time: 23.587 s (1025 ms/file) [testng] [2024-10-09 06:15:36,580] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-09 06:16:33,182] [pool-1-thread-1] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_100.hdr: [testng] 06:16:33,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 06:16:33,182 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:16:33,184 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-09_06-16-33.log] [testng] 06:16:33,184 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4cc88342 - End of configuration. [testng] [2024-10-09 06:16:34,494] [pool-1-thread-12] Initializing /data/public/NIH/zstat1.nii: [testng] 06:16:34,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 06:16:34,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:16:34,496 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-09_06-16-34.log] [testng] 06:16:34,496 |-INFO in ch.qos.logback.core.sift.SiftProcessor@de3c38a - End of configuration. [testng] [2024-10-09 06:16:35,766] [pool-1-thread-11] Initializing /data/public/NIH/avg152T1_LR_nifti.nii: [testng] 06:16:35,766 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 06:16:35,766 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:16:35,767 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-09_06-16-35.log] [testng] 06:16:35,767 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ad1edff - End of configuration. [testng] [2024-10-09 06:16:36,940] [pool-1-thread-10] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_100.hdr: [testng] 06:16:36,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 06:16:36,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:16:36,941 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-09_06-16-36.log] [testng] 06:16:36,942 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35e69282 - End of configuration. [testng] [2024-10-09 06:16:38,265] [pool-1-thread-9] Initializing /data/public/NIH/zstat1.nii.gz: [testng] 06:16:38,265 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 06:16:38,265 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:16:38,266 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-09_06-16-38.log] [testng] 06:16:38,266 |-INFO in ch.qos.logback.core.sift.SiftProcessor@408a20ae - End of configuration. [testng] [2024-10-09 06:16:43,476] [pool-1-thread-8] Initializing /data/public/NIH/avg152T1_LR_nifti.nii.gz: [testng] 06:16:43,476 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 06:16:43,476 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:16:43,477 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-09_06-16-43.log] [testng] 06:16:43,477 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2540d21d - End of configuration. [testng] [2024-10-09 06:16:48,901] [pool-1-thread-7] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_94.hdr: [testng] 06:16:48,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 06:16:48,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:16:48,902 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-09_06-16-48.log] [testng] 06:16:48,902 |-INFO in ch.qos.logback.core.sift.SiftProcessor@16bb1278 - End of configuration. [testng] [2024-10-09 06:16:50,116] [pool-1-thread-6] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_27_conf_86.hdr: [testng] 06:16:50,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 06:16:50,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:16:50,117 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-09_06-16-50.log] [testng] 06:16:50,117 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d427a9e - End of configuration. [testng] [2024-10-09 06:16:51,360] [pool-1-thread-5] Initializing /data/public/NIH/filtered_func_data.nii: [testng] 06:16:51,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 06:16:51,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:16:51,361 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-09_06-16-51.log] [testng] 06:16:51,362 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d5e77fb - End of configuration. [testng] [2024-10-09 06:16:52,563] [pool-1-thread-4] Initializing /data/public/NIH/avg152T1_RL_nifti.nii: [testng] 06:16:52,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 06:16:52,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:16:52,564 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-09_06-16-52.log] [testng] 06:16:52,564 |-INFO in ch.qos.logback.core.sift.SiftProcessor@446d5c89 - End of configuration. [testng] [2024-10-09 06:16:53,853] [pool-1-thread-3] Initializing /data/public/NIH/avg152T1_RL_nifti.hdr: [testng] 06:16:53,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 06:16:53,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:16:53,854 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-09_06-16-53.log] [testng] 06:16:53,854 |-INFO in ch.qos.logback.core.sift.SiftProcessor@31bf09ca - End of configuration. [testng] [2024-10-09 06:16:55,164] [pool-1-thread-2] Initializing /data/public/NIH/newsirp_final_XML.nii: [testng] 06:16:55,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 06:16:55,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:16:55,165 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-09_06-16-55.log] [testng] 06:16:55,165 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c0d4ea3 - End of configuration. [testng] [2024-10-09 06:17:04,910] [pool-1-thread-12] Initializing /data/public/NIH/filtered_func_data.nii.gz: [testng] [2024-10-09 06:17:12,488] [pool-1-thread-4] Initializing /data/public/NIH/avg152T1_RL_nifti.nii.gz: [testng] [2024-10-09 06:17:17,757] [pool-1-thread-11] Initializing /data/public/NIH/minimal.nii: [testng] [2024-10-09 06:17:18,967] [pool-1-thread-5] Initializing /data/public/NIH/avg152T1_LR_nifti.hdr: [testng] [2024-10-09 06:17:20,197] [pool-1-thread-2] Initializing /data/qa-17334/volume4d.nii: [testng] [2024-10-09 06:17:24,953] [pool-1-thread-3] Initializing /data/public/NIH/minimal.hdr: [testng] [2024-10-09 06:17:26,286] [pool-1-thread-6] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_94.hdr: [testng] [2024-10-09 06:17:27,544] [pool-1-thread-7] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_26_conf_91.hdr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1060, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 3 minutes 5 seconds Finished: SUCCESS