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Started by upstream project "BIOFORMATS-test-repo" build number 31 originally caused by: Started by upstream project "Trigger" build number 35 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins2197096956852600660.sh + '[' nifti = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_4221_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 test-automated: [testng] File leak detector installed [testng] 08:40:29,911 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 08:40:29,913 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 08:40:29,913 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 08:40:29,914 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 08:40:29,914 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 08:40:29,914 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 08:40:29,915 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 08:40:29,915 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 08:40:29,915 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 08:40:29,916 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 08:40:29,916 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 08:40:29,916 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 08:40:30,177 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 08:40:30,177 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 08:40:30,205 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 08:40:30,206 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 08:40:30,214 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 08:40:30,214 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 08:40:30,214 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 08:40:30,215 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 08:40:30,215 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 08:40:30,215 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 08:40:30,216 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 301 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-12 08:40:30,226] [main] java.version = 1.8.0_342 [testng] 08:40:30,229 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 08:40:30,229 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:40:30,275 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-12_08-40-30.log] [testng] 08:40:30,276 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-04-12 08:40:30,278] [main] testng.directory = /data [testng] [2024-04-12 08:40:30,279] [main] testng.configDirectory = /config [testng] [2024-04-12 08:40:30,292] [main] testng.multiplier = 1.0 [testng] [2024-04-12 08:40:30,292] [main] testng.in-memory = false [testng] [2024-04-12 08:40:30,292] [main] testng.allow-missing = false [testng] [2024-04-12 08:40:30,292] [main] user.language = en [testng] [2024-04-12 08:40:30,292] [main] user.country = ${user.country} [testng] [2024-04-12 08:40:30,292] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-04-12 08:40:31,144] [main] ---------------------------------------- [testng] [2024-04-12 08:40:31,144] [main] Total files: 23 [testng] [2024-04-12 08:40:31,144] [main] Scan time: 0.852 s (37 ms/file) [testng] [2024-04-12 08:40:31,144] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-12 08:40:35,943] [pool-1-thread-1] Initializing /data/public/NIH/filtered_func_data.nii.gz: [testng] 08:40:35,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 08:40:35,943 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:40:35,944 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-12_08-40-35.log] [testng] 08:40:35,944 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d92dbfd - End of configuration. [testng] [2024-04-12 08:40:38,907] [pool-1-thread-12] Initializing /data/public/NIH/minimal.nii: [testng] 08:40:38,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 08:40:38,907 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:40:38,908 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-12_08-40-38.log] [testng] 08:40:38,908 |-INFO in ch.qos.logback.core.sift.SiftProcessor@719dab97 - End of configuration. [testng] [2024-04-12 08:40:38,922] [pool-1-thread-11] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_94.hdr: [testng] 08:40:38,922 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 08:40:38,922 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:40:38,923 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-12_08-40-38.log] [testng] 08:40:38,923 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a538da8 - End of configuration. [testng] [2024-04-12 08:40:38,932] [pool-1-thread-10] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_100.hdr: [testng] 08:40:38,933 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 08:40:38,933 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:40:38,933 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-12_08-40-38.log] [testng] 08:40:38,933 |-INFO in ch.qos.logback.core.sift.SiftProcessor@576477ae - End of configuration. [testng] [2024-04-12 08:40:38,946] [pool-1-thread-9] Initializing /data/qa-17334/volume4d.nii: [testng] 08:40:38,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 08:40:38,946 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:40:38,947 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-12_08-40-38.log] [testng] 08:40:38,947 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fa51957 - End of configuration. [testng] [2024-04-12 08:40:38,964] [pool-1-thread-8] Initializing /data/public/NIH/avg152T1_RL_nifti.nii.gz: [testng] 08:40:38,964 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 08:40:38,964 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:40:38,965 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-12_08-40-38.log] [testng] 08:40:38,965 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5466f3e2 - End of configuration. [testng] [2024-04-12 08:40:39,162] [pool-1-thread-7] Initializing /data/public/NIH/avg152T1_LR_nifti.nii.gz: [testng] 08:40:39,162 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 08:40:39,162 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:40:39,163 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-12_08-40-39.log] [testng] 08:40:39,163 |-INFO in ch.qos.logback.core.sift.SiftProcessor@350bea04 - End of configuration. [testng] [2024-04-12 08:40:39,378] [pool-1-thread-6] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_94.hdr: [testng] 08:40:39,379 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 08:40:39,379 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:40:39,379 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-12_08-40-39.log] [testng] 08:40:39,379 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1eef6903 - End of configuration. [testng] [2024-04-12 08:40:39,389] [pool-1-thread-5] Initializing /data/public/NIH/filtered_func_data.nii: [testng] 08:40:39,389 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 08:40:39,389 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:40:39,389 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-12_08-40-39.log] [testng] 08:40:39,390 |-INFO in ch.qos.logback.core.sift.SiftProcessor@486117b5 - End of configuration. [testng] [2024-04-12 08:40:39,408] [pool-1-thread-4] Initializing /data/public/NIH/avg152T1_LR_nifti.nii: [testng] 08:40:39,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 08:40:39,408 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:40:39,408 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-12_08-40-39.log] [testng] 08:40:39,409 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ce3049e - End of configuration. [testng] [2024-04-12 08:40:39,424] [pool-1-thread-3] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_100.hdr: [testng] 08:40:39,424 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 08:40:39,424 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:40:39,425 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-12_08-40-39.log] [testng] 08:40:39,425 |-INFO in ch.qos.logback.core.sift.SiftProcessor@722016ab - End of configuration. [testng] [2024-04-12 08:40:39,434] [pool-1-thread-2] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_27_conf_86.hdr: [testng] 08:40:39,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 08:40:39,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:40:39,435 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-12_08-40-39.log] [testng] 08:40:39,435 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2fa92f05 - End of configuration. [testng] [2024-04-12 08:40:40,594] [pool-1-thread-10] Initializing /data/public/NIH/zstat1.nii: [testng] [2024-04-12 08:40:40,608] [pool-1-thread-4] Initializing /data/public/NIH/newsirp_final_XML.nii: [testng] [2024-04-12 08:40:40,627] [pool-1-thread-3] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_26_conf_91.hdr: [testng] [2024-04-12 08:40:40,636] [pool-1-thread-2] Initializing /data/public/NIH/zstat1.nii.gz: [testng] [2024-04-12 08:40:40,723] [pool-1-thread-11] Initializing /data/public/NIH/avg152T1_LR_nifti.hdr: [testng] [2024-04-12 08:40:40,735] [pool-1-thread-6] Initializing /data/public/NIH/avg152T1_RL_nifti.hdr: [testng] [2024-04-12 08:40:40,742] [pool-1-thread-9] Initializing /data/public/NIH/minimal.hdr: [testng] [2024-04-12 08:40:40,752] [pool-1-thread-5] Initializing /data/public/NIH/avg152T1_RL_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: 43 seconds Finished: SUCCESS