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Started by upstream project "BIOFORMATS-test-repo" build number 23 originally caused by: Started by upstream project "Trigger" build number 26 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/jenkins5354627137781319013.sh + '[' nifti = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_2909_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] 02:36:52,142 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:36:52,144 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 02:36:52,144 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:36:52,145 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:36:52,146 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:36:52,146 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:36:52,146 |-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] 02:36:52,146 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:36:52,147 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:36:52,147 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:36:52,147 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:36:52,147 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:36:52,387 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:36:52,387 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:36:52,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:36:52,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:36:52,426 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:36:52,427 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:36:52,427 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:36:52,427 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:36:52,427 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 02:36:52,428 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 02:36:52,428 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 281 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-05 02:36:52,439] [main] java.version = 1.8.0_342 [testng] 02:36:52,443 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:36:52,443 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:36:52,490 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-05_02-36-52.log] [testng] 02:36:52,491 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-04-05 02:36:52,494] [main] testng.directory = /data [testng] [2024-04-05 02:36:52,494] [main] testng.configDirectory = /config [testng] [2024-04-05 02:36:52,506] [main] testng.multiplier = 1.0 [testng] [2024-04-05 02:36:52,507] [main] testng.in-memory = false [testng] [2024-04-05 02:36:52,507] [main] testng.allow-missing = false [testng] [2024-04-05 02:36:52,507] [main] user.language = en [testng] [2024-04-05 02:36:52,507] [main] user.country = ${user.country} [testng] [2024-04-05 02:36:52,507] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-04-05 02:36:53,424] [main] ---------------------------------------- [testng] [2024-04-05 02:36:53,424] [main] Total files: 23 [testng] [2024-04-05 02:36:53,424] [main] Scan time: 0.917 s (39 ms/file) [testng] [2024-04-05 02:36:53,424] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-05 02:36:58,435] [pool-1-thread-1] Initializing /data/public/NIH/filtered_func_data.nii.gz: [testng] 02:36:58,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:36:58,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:36:58,436 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-05_02-36-58.log] [testng] 02:36:58,437 |-INFO in ch.qos.logback.core.sift.SiftProcessor@403269ef - End of configuration. [testng] [2024-04-05 02:37:01,360] [pool-1-thread-12] Initializing /data/public/NIH/minimal.nii: [testng] 02:37:01,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:37:01,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:37:01,361 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-05_02-37-01.log] [testng] 02:37:01,362 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f9377e3 - End of configuration. [testng] [2024-04-05 02:37:01,372] [pool-1-thread-11] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_94.hdr: [testng] 02:37:01,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:37:01,372 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:37:01,373 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-05_02-37-01.log] [testng] 02:37:01,373 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5367d4f2 - End of configuration. [testng] [2024-04-05 02:37:01,384] [pool-1-thread-10] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_100.hdr: [testng] 02:37:01,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:37:01,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:37:01,385 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-05_02-37-01.log] [testng] 02:37:01,385 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1589809c - End of configuration. [testng] [2024-04-05 02:37:01,397] [pool-1-thread-9] Initializing /data/qa-17334/volume4d.nii: [testng] 02:37:01,397 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:37:01,397 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:37:01,397 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-05_02-37-01.log] [testng] 02:37:01,398 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a191272 - End of configuration. [testng] [2024-04-05 02:37:01,418] [pool-1-thread-8] Initializing /data/public/NIH/avg152T1_RL_nifti.nii.gz: [testng] 02:37:01,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:37:01,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:37:01,418 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-05_02-37-01.log] [testng] 02:37:01,419 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e5ecb05 - End of configuration. [testng] [2024-04-05 02:37:01,612] [pool-1-thread-7] Initializing /data/public/NIH/avg152T1_LR_nifti.nii.gz: [testng] 02:37:01,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:37:01,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:37:01,613 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-05_02-37-01.log] [testng] 02:37:01,614 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a7ac56a - End of configuration. [testng] [2024-04-05 02:37:01,826] [pool-1-thread-6] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_94.hdr: [testng] 02:37:01,826 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:37:01,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:37:01,827 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-05_02-37-01.log] [testng] 02:37:01,828 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b975c30 - End of configuration. [testng] [2024-04-05 02:37:01,840] [pool-1-thread-5] Initializing /data/public/NIH/filtered_func_data.nii: [testng] 02:37:01,840 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:37:01,841 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:37:01,841 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-05_02-37-01.log] [testng] 02:37:01,842 |-INFO in ch.qos.logback.core.sift.SiftProcessor@647eeff2 - End of configuration. [testng] [2024-04-05 02:37:01,859] [pool-1-thread-4] Initializing /data/public/NIH/avg152T1_LR_nifti.nii: [testng] 02:37:01,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:37:01,859 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:37:01,860 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-05_02-37-01.log] [testng] 02:37:01,860 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3af62591 - End of configuration. [testng] [2024-04-05 02:37:01,874] [pool-1-thread-3] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_100.hdr: [testng] 02:37:01,874 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:37:01,874 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:37:01,875 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-05_02-37-01.log] [testng] 02:37:01,875 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d51c603 - End of configuration. [testng] [2024-04-05 02:37:01,886] [pool-1-thread-2] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_27_conf_86.hdr: [testng] 02:37:01,887 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:37:01,887 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:37:01,887 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-05_02-37-01.log] [testng] 02:37:01,888 |-INFO in ch.qos.logback.core.sift.SiftProcessor@153c3e4b - End of configuration. [testng] [2024-04-05 02:37:02,975] [pool-1-thread-10] Initializing /data/public/NIH/zstat1.nii: [testng] [2024-04-05 02:37:02,988] [pool-1-thread-3] Initializing /data/public/NIH/newsirp_final_XML.nii: [testng] [2024-04-05 02:37:03,006] [pool-1-thread-2] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_26_conf_91.hdr: [testng] [2024-04-05 02:37:03,014] [pool-1-thread-12] Initializing /data/public/NIH/zstat1.nii.gz: [testng] [2024-04-05 02:37:03,080] [pool-1-thread-6] Initializing /data/public/NIH/avg152T1_LR_nifti.hdr: [testng] [2024-04-05 02:37:03,088] [pool-1-thread-11] Initializing /data/public/NIH/avg152T1_RL_nifti.hdr: [testng] [2024-04-05 02:37:03,098] [pool-1-thread-5] Initializing /data/public/NIH/minimal.hdr: [testng] [2024-04-05 02:37:03,109] [pool-1-thread-4] 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: 42 seconds Finished: SUCCESS