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Started by upstream project "BIOFORMATS-test-repo" build number 35 originally caused by: Started by upstream project "Trigger" build number 39 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins8445048120226346253.sh + '[' nifti = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_4877_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 -Duser.language=fr -Duser.country=FR 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] 13:25:40,129 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 13:25:40,130 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 13:25:40,130 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 13:25:40,131 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 13:25:40,131 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 13:25:40,132 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 13:25:40,132 |-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] 13:25:40,132 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 13:25:40,132 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 13:25:40,133 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 13:25:40,133 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 13:25:40,133 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 13:25:40,350 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 13:25:40,350 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 13:25:40,377 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 13:25:40,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 13:25:40,385 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 13:25:40,386 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 13:25:40,386 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 13:25:40,386 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 13:25:40,386 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 13:25:40,387 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 13:25:40,387 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 255 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-04-15 13:25:40,396] [main] java.version = 1.8.0_342 [testng] 13:25:40,400 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 13:25:40,400 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:25:40,443 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-04-15_13-25-40.log] [testng] 13:25:40,445 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-04-15 13:25:40,446] [main] testng.directory = /data [testng] [2024-04-15 13:25:40,447] [main] testng.configDirectory = /config [testng] [2024-04-15 13:25:40,458] [main] testng.multiplier = 1.0 [testng] [2024-04-15 13:25:40,459] [main] testng.in-memory = false [testng] [2024-04-15 13:25:40,459] [main] testng.allow-missing = false [testng] [2024-04-15 13:25:40,459] [main] user.language = fr [testng] [2024-04-15 13:25:40,459] [main] user.country = FR [testng] [2024-04-15 13:25:40,459] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-04-15 13:25:41,320] [main] ---------------------------------------- [testng] [2024-04-15 13:25:41,320] [main] Total files: 23 [testng] [2024-04-15 13:25:41,320] [main] Scan time: 0.861 s (37 ms/file) [testng] [2024-04-15 13:25:41,321] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-04-15 13:25:46,207] [pool-1-thread-1] Initializing /data/public/NIH/filtered_func_data.nii.gz: [testng] 13:25:46,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 13:25:46,208 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:25:46,208 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-04-15_13-25-46.log] [testng] 13:25:46,209 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b5bfa3d - End of configuration. [testng] [2024-04-15 13:25:49,139] [pool-1-thread-12] Initializing /data/public/NIH/minimal.nii: [testng] 13:25:49,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 13:25:49,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:25:49,140 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-04-15_13-25-49.log] [testng] 13:25:49,140 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35755e10 - End of configuration. [testng] [2024-04-15 13:25:49,151] [pool-1-thread-11] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_94.hdr: [testng] 13:25:49,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 13:25:49,151 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:25:49,152 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-04-15_13-25-49.log] [testng] 13:25:49,152 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d5cc9a7 - End of configuration. [testng] [2024-04-15 13:25:49,165] [pool-1-thread-10] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_100.hdr: [testng] 13:25:49,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 13:25:49,166 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:25:49,167 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-04-15_13-25-49.log] [testng] 13:25:49,167 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7277f748 - End of configuration. [testng] [2024-04-15 13:25:49,181] [pool-1-thread-9] Initializing /data/qa-17334/volume4d.nii: [testng] 13:25:49,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 13:25:49,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:25:49,181 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-04-15_13-25-49.log] [testng] 13:25:49,182 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d3c001d - End of configuration. [testng] [2024-04-15 13:25:49,198] [pool-1-thread-8] Initializing /data/public/NIH/avg152T1_RL_nifti.nii.gz: [testng] 13:25:49,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 13:25:49,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:25:49,199 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-04-15_13-25-49.log] [testng] 13:25:49,200 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a9cffce - End of configuration. [testng] [2024-04-15 13:25:49,400] [pool-1-thread-7] Initializing /data/public/NIH/avg152T1_LR_nifti.nii.gz: [testng] 13:25:49,400 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 13:25:49,400 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:25:49,401 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-04-15_13-25-49.log] [testng] 13:25:49,401 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5367d4f2 - End of configuration. [testng] [2024-04-15 13:25:49,595] [pool-1-thread-6] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_94.hdr: [testng] 13:25:49,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 13:25:49,596 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:25:49,596 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-04-15_13-25-49.log] [testng] 13:25:49,597 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2796d2d0 - End of configuration. [testng] [2024-04-15 13:25:49,605] [pool-1-thread-5] Initializing /data/public/NIH/filtered_func_data.nii: [testng] 13:25:49,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 13:25:49,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:25:49,606 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-04-15_13-25-49.log] [testng] 13:25:49,607 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62150b7f - End of configuration. [testng] [2024-04-15 13:25:49,623] [pool-1-thread-4] Initializing /data/public/NIH/avg152T1_LR_nifti.nii: [testng] 13:25:49,623 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 13:25:49,623 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:25:49,623 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-04-15_13-25-49.log] [testng] 13:25:49,624 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f1b97f5 - End of configuration. [testng] [2024-04-15 13:25:49,638] [pool-1-thread-3] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_100.hdr: [testng] 13:25:49,638 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 13:25:49,638 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:25:49,639 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-04-15_13-25-49.log] [testng] 13:25:49,639 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e5ecb05 - End of configuration. [testng] [2024-04-15 13:25:49,649] [pool-1-thread-2] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_27_conf_86.hdr: [testng] 13:25:49,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 13:25:49,650 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:25:49,650 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-04-15_13-25-49.log] [testng] 13:25:49,650 |-INFO in ch.qos.logback.core.sift.SiftProcessor@647eeff2 - End of configuration. [testng] [2024-04-15 13:25:50,844] [pool-1-thread-12] Initializing /data/public/NIH/zstat1.nii: [testng] [2024-04-15 13:25:50,857] [pool-1-thread-4] Initializing /data/public/NIH/newsirp_final_XML.nii: [testng] [2024-04-15 13:25:50,874] [pool-1-thread-6] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_26_conf_91.hdr: [testng] [2024-04-15 13:25:50,885] [pool-1-thread-10] Initializing /data/public/NIH/zstat1.nii.gz: [testng] [2024-04-15 13:25:50,958] [pool-1-thread-11] Initializing /data/public/NIH/avg152T1_LR_nifti.hdr: [testng] [2024-04-15 13:25:50,967] [pool-1-thread-3] Initializing /data/public/NIH/avg152T1_RL_nifti.hdr: [testng] [2024-04-15 13:25:50,977] [pool-1-thread-9] Initializing /data/public/NIH/minimal.hdr: [testng] [2024-04-15 13:25:50,986] [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