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Started by upstream project "BIOFORMATS-test-repo" build number 208 originally caused by: Started by upstream project "Trigger" build number 234 originally caused by: Started by timer 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/jenkins17215332329825671602.sh + '[' nifti = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_33093_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 05:20:57,559 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 05:20:57,561 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 05:20:57,561 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:20:57,561 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:20:57,562 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 05:20:57,562 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 05:20:57,562 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 05:20:57,562 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:20:57,563 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:20:57,563 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 05:20:57,564 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 05:20:57,564 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 05:20:57,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 05:20:57,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 05:20:57,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 05:20:57,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 05:20:57,744 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 05:20:57,744 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 05:20:57,744 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 05:20:57,745 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 05:20:57,745 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 05:20:57,745 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 05:20:57,746 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 183 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-03 05:20:57,754] [main] java.version = 21 [testng] 05:20:57,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:20:57,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:20:57,797 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-03_05-20-57.log] [testng] 05:20:57,798 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-10-03 05:20:57,800] [main] testng.directory = /data [testng] [2024-10-03 05:20:57,800] [main] testng.configDirectory = /config [testng] [2024-10-03 05:20:57,808] [main] testng.multiplier = 1.0 [testng] [2024-10-03 05:20:57,808] [main] testng.in-memory = false [testng] [2024-10-03 05:20:57,808] [main] testng.allow-missing = false [testng] [2024-10-03 05:20:57,809] [main] user.language = en [testng] [2024-10-03 05:20:57,809] [main] user.country = ${user.country} [testng] [2024-10-03 05:20:57,809] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-03 05:21:07,877] [main] ---------------------------------------- [testng] [2024-10-03 05:21:07,877] [main] Total files: 23 [testng] [2024-10-03 05:21:07,877] [main] Scan time: 10.068 s (437 ms/file) [testng] [2024-10-03 05:21:07,878] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-03 05:21:34,115] [pool-1-thread-1] Initializing /data/public/NIH/minimal.hdr: [testng] 05:21:34,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 05:21:34,116 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:21:34,117 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-03_05-21-34.log] [testng] 05:21:34,118 |-INFO in ch.qos.logback.core.sift.SiftProcessor@539fe98b - End of configuration. [testng] [2024-10-03 05:21:34,694] [pool-1-thread-12] Initializing /data/public/NIH/minimal.nii: [testng] 05:21:34,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 05:21:34,694 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:21:34,704 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-03_05-21-34.log] [testng] 05:21:34,705 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69313113 - End of configuration. [testng] [2024-10-03 05:21:35,210] [pool-1-thread-11] Initializing /data/public/NIH/filtered_func_data.nii.gz: [testng] 05:21:35,210 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 05:21:35,210 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:21:35,211 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-03_05-21-35.log] [testng] 05:21:35,211 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7147df0c - End of configuration. [testng] [2024-10-03 05:21:40,069] [pool-1-thread-10] Initializing /data/public/NIH/avg152T1_RL_nifti.nii.gz: [testng] 05:21:40,069 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 05:21:40,070 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:21:40,071 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-03_05-21-40.log] [testng] 05:21:40,071 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f309c6e - End of configuration. [testng] [2024-10-03 05:21:42,520] [pool-1-thread-9] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_100.hdr: [testng] 05:21:42,520 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 05:21:42,520 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:21:42,520 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-03_05-21-42.log] [testng] 05:21:42,521 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b1135d4 - End of configuration. [testng] [2024-10-03 05:21:43,083] [pool-1-thread-8] Initializing /data/public/NIH/avg152T1_LR_nifti.nii.gz: [testng] 05:21:43,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 05:21:43,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:21:43,084 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-03_05-21-43.log] [testng] 05:21:43,085 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66e9d90d - End of configuration. [testng] [2024-10-03 05:21:45,400] [pool-1-thread-7] Initializing /data/public/NIH/avg152T1_LR_nifti.nii: [testng] 05:21:45,400 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 05:21:45,400 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:21:45,401 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-03_05-21-45.log] [testng] 05:21:45,401 |-INFO in ch.qos.logback.core.sift.SiftProcessor@192039d - End of configuration. [testng] [2024-10-03 05:21:45,886] [pool-1-thread-6] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_94.hdr: [testng] 05:21:45,886 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 05:21:45,886 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:21:45,887 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-03_05-21-45.log] [testng] 05:21:45,887 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55f85846 - End of configuration. [testng] [2024-10-03 05:21:46,419] [pool-1-thread-5] Initializing /data/public/NIH/avg152T1_RL_nifti.hdr: [testng] 05:21:46,419 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 05:21:46,419 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:21:46,420 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-03_05-21-46.log] [testng] 05:21:46,420 |-INFO in ch.qos.logback.core.sift.SiftProcessor@590fa094 - End of configuration. [testng] [2024-10-03 05:21:46,949] [pool-1-thread-4] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_94.hdr: [testng] 05:21:46,949 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 05:21:46,950 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:21:46,950 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-03_05-21-46.log] [testng] 05:21:46,950 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a398a4d - End of configuration. [testng] [2024-10-03 05:21:47,467] [pool-1-thread-3] Initializing /data/qa-17334/volume4d.nii: [testng] 05:21:47,467 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 05:21:47,468 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:21:47,468 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-03_05-21-47.log] [testng] 05:21:47,468 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9064892 - End of configuration. [testng] [2024-10-03 05:21:47,967] [pool-1-thread-2] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_100.hdr: [testng] 05:21:47,967 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 05:21:47,967 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:21:47,968 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-03_05-21-47.log] [testng] 05:21:47,968 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e31cb29 - End of configuration. [testng] [2024-10-03 05:21:53,050] [pool-1-thread-12] Initializing /data/public/NIH/zstat1.nii: [testng] [2024-10-03 05:21:53,609] [pool-1-thread-7] Initializing /data/public/NIH/avg152T1_RL_nifti.nii: [testng] [2024-10-03 05:21:54,158] [pool-1-thread-3] Initializing /data/public/NIH/avg152T1_LR_nifti.hdr: [testng] [2024-10-03 05:21:56,718] [pool-1-thread-1] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_27_conf_86.hdr: [testng] [2024-10-03 05:21:57,292] [pool-1-thread-6] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_26_conf_91.hdr: [testng] [2024-10-03 05:21:57,880] [pool-1-thread-4] Initializing /data/public/NIH/zstat1.nii.gz: [testng] [2024-10-03 05:22:00,097] [pool-1-thread-9] Initializing /data/public/NIH/filtered_func_data.nii: [testng] [2024-10-03 05:22:00,627] [pool-1-thread-2] Initializing /data/public/NIH/newsirp_final_XML.nii: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1060, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 1 minute 33 seconds Finished: SUCCESS