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Started by upstream project "BIOFORMATS-test-repo" build number 263 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/jenkins1653185638617250896.sh + '[' nifti = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_41597_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings 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] 20:40:54,516 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 20:40:54,517 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 20:40:54,517 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 20:40:54,518 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 20:40:54,519 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 20:40:54,519 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 20:40:54,519 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 20:40:54,519 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 20:40:54,520 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 20:40:54,520 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 20:40:54,520 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 20:40:54,521 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 20:40:54,667 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 20:40:54,667 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 20:40:54,690 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 20:40:54,690 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 20:40:54,696 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 20:40:54,696 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 20:40:54,696 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 20:40:54,696 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 20:40:54,696 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 20:40:54,697 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 20:40:54,697 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 177 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-21 20:40:54,706] [main] java.version = 21 [testng] 20:40:54,708 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 20:40:54,709 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:40:54,747 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-21_20-40-54.log] [testng] 20:40:54,748 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-11-21 20:40:54,750] [main] testng.directory = /data [testng] [2024-11-21 20:40:54,750] [main] testng.configDirectory = /config [testng] [2024-11-21 20:40:54,758] [main] testng.multiplier = 1.0 [testng] [2024-11-21 20:40:54,758] [main] testng.in-memory = false [testng] [2024-11-21 20:40:54,758] [main] testng.allow-missing = false [testng] [2024-11-21 20:40:54,759] [main] user.language = en [testng] [2024-11-21 20:40:54,759] [main] user.country = ${user.country} [testng] [2024-11-21 20:40:54,759] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-21 20:41:08,893] [main] ---------------------------------------- [testng] [2024-11-21 20:41:08,893] [main] Total files: 23 [testng] [2024-11-21 20:41:08,893] [main] Scan time: 14.134 s (614 ms/file) [testng] [2024-11-21 20:41:08,893] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-21 20:41:46,701] [pool-1-thread-1] Initializing /data/public/NIH/minimal.hdr: [testng] 20:41:46,701 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 20:41:46,701 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:41:46,702 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-21_20-41-46.log] [testng] 20:41:46,703 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23aace58 - End of configuration. [testng] [2024-11-21 20:41:47,555] [pool-1-thread-12] Initializing /data/public/NIH/minimal.nii: [testng] 20:41:47,556 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 20:41:47,556 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:41:47,563 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-21_20-41-47.log] [testng] 20:41:47,563 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b0f8cd4 - End of configuration. [testng] [2024-11-21 20:41:48,367] [pool-1-thread-11] Initializing /data/public/NIH/avg152T1_RL_nifti.nii.gz: [testng] 20:41:48,367 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 20:41:48,367 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:41:48,368 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-21_20-41-48.log] [testng] 20:41:48,369 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14e65859 - End of configuration. [testng] [2024-11-21 20:41:51,712] [pool-1-thread-10] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_27_conf_86.hdr: [testng] 20:41:51,712 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 20:41:51,712 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:41:51,713 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-21_20-41-51.log] [testng] 20:41:51,713 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5aa14768 - End of configuration. [testng] [2024-11-21 20:41:52,562] [pool-1-thread-9] Initializing /data/public/NIH/newsirp_final_XML.nii: [testng] 20:41:52,562 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 20:41:52,562 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:41:52,563 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-21_20-41-52.log] [testng] 20:41:52,563 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2fb92bee - End of configuration. [testng] [2024-11-21 20:41:53,348] [pool-1-thread-8] Initializing /data/public/NIH/zstat1.nii: [testng] 20:41:53,348 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 20:41:53,348 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:41:53,349 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-21_20-41-53.log] [testng] 20:41:53,349 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7725333a - End of configuration. [testng] [2024-11-21 20:41:54,092] [pool-1-thread-7] Initializing /data/public/NIH/avg152T1_RL_nifti.nii: [testng] 20:41:54,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 20:41:54,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:41:54,093 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-21_20-41-54.log] [testng] 20:41:54,093 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a6cf4c2 - End of configuration. [testng] [2024-11-21 20:41:54,842] [pool-1-thread-6] Initializing /data/public/NIH/avg152T1_LR_nifti.hdr: [testng] 20:41:54,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 20:41:54,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:41:54,843 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-21_20-41-54.log] [testng] 20:41:54,843 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d00e4b7 - End of configuration. [testng] [2024-11-21 20:41:55,679] [pool-1-thread-5] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_100.hdr: [testng] 20:41:55,679 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 20:41:55,679 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:41:55,679 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-21_20-41-55.log] [testng] 20:41:55,680 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3856a1ff - End of configuration. [testng] [2024-11-21 20:41:56,502] [pool-1-thread-4] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_94.hdr: [testng] 20:41:56,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 20:41:56,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:41:56,503 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-21_20-41-56.log] [testng] 20:41:56,503 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fad7e21 - End of configuration. [testng] [2024-11-21 20:41:57,292] [pool-1-thread-3] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_94.hdr: [testng] 20:41:57,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 20:41:57,292 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:41:57,292 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-21_20-41-57.log] [testng] 20:41:57,293 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8a65d62 - End of configuration. [testng] [2024-11-21 20:41:58,112] [pool-1-thread-2] Initializing /data/public/NIH/filtered_func_data.nii.gz: [testng] 20:41:58,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 20:41:58,113 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 20:41:58,113 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-21_20-41-58.log] [testng] 20:41:58,114 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b3bab6d - End of configuration. [testng] [2024-11-21 20:42:10,714] [pool-1-thread-12] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_100.hdr: [testng] [2024-11-21 20:42:11,517] [pool-1-thread-8] Initializing /data/public/NIH/filtered_func_data.nii: [testng] [2024-11-21 20:42:12,434] [pool-1-thread-7] Initializing /data/public/NIH/avg152T1_LR_nifti.nii.gz: [testng] [2024-11-21 20:42:15,667] [pool-1-thread-9] Initializing /data/public/NIH/avg152T1_RL_nifti.hdr: [testng] [2024-11-21 20:42:17,829] [pool-1-thread-5] Initializing /data/qa-17334/volume4d.nii: [testng] [2024-11-21 20:42:18,714] [pool-1-thread-1] Initializing /data/public/NIH/zstat1.nii.gz: [testng] [2024-11-21 20:42:21,914] [pool-1-thread-6] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_26_conf_91.hdr: [testng] [2024-11-21 20:42:22,665] [pool-1-thread-10] Initializing /data/public/NIH/avg152T1_LR_nifti.nii: [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 2 seconds Finished: SUCCESS