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Started by upstream project "BIOFORMATS-test-repo" build number 7 originally caused by: Started by upstream project "Trigger" build number 10 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins4795069895863849175.sh + '[' nifti = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_1046_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 07:39:48,923 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 07:39:48,924 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 07:39:48,924 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 07:39:48,925 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 07:39:48,926 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 07:39:48,926 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 07:39:48,927 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 07:39:48,927 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 07:39:48,927 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 07:39:48,928 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 07:39:48,928 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 07:39:48,928 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 07:39:49,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 07:39:49,139 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 07:39:49,172 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 07:39:49,172 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 07:39:49,179 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 07:39:49,179 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 07:39:49,179 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 07:39:49,179 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 07:39:49,179 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 07:39:49,180 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 07:39:49,180 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 253 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-21 07:39:49,190] [main] java.version = 21 [testng] 07:39:49,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 07:39:49,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:39:49,240 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-21_07-39-49.log] [testng] 07:39:49,241 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-03-21 07:39:49,243] [main] testng.directory = /data [testng] [2024-03-21 07:39:49,243] [main] testng.configDirectory = /config [testng] [2024-03-21 07:39:49,253] [main] testng.multiplier = 1.0 [testng] [2024-03-21 07:39:49,253] [main] testng.in-memory = false [testng] [2024-03-21 07:39:49,253] [main] testng.allow-missing = false [testng] [2024-03-21 07:39:49,254] [main] user.language = en [testng] [2024-03-21 07:39:49,254] [main] user.country = ${user.country} [testng] [2024-03-21 07:39:49,254] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-21 07:39:50,661] [main] ---------------------------------------- [testng] [2024-03-21 07:39:50,661] [main] Total files: 23 [testng] [2024-03-21 07:39:50,661] [main] Scan time: 1.407 s (61 ms/file) [testng] [2024-03-21 07:39:50,662] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-21 07:39:58,483] [pool-1-thread-1] Initializing /data/public/NIH/avg152T1_LR_nifti.hdr: [testng] 07:39:58,484 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 07:39:58,484 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:39:58,486 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-21_07-39-58.log] [testng] 07:39:58,486 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12ee0843 - End of configuration. [testng] [2024-03-21 07:39:58,532] [pool-1-thread-12] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_27_conf_86.hdr: [testng] 07:39:58,532 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 07:39:58,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:39:58,534 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-21_07-39-58.log] [testng] 07:39:58,545 |-INFO in ch.qos.logback.core.sift.SiftProcessor@285059ab - End of configuration. [testng] [2024-03-21 07:39:58,573] [pool-1-thread-11] Initializing /data/qa-17334/volume4d.nii: [testng] 07:39:58,573 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 07:39:58,573 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:39:58,574 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-21_07-39-58.log] [testng] 07:39:58,575 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f3922fa - End of configuration. [testng] [2024-03-21 07:39:58,614] [pool-1-thread-10] Initializing /data/public/NIH/avg152T1_LR_nifti.nii.gz: [testng] 07:39:58,615 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 07:39:58,615 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:39:58,616 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-21_07-39-58.log] [testng] 07:39:58,616 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10ee589 - End of configuration. [testng] [2024-03-21 07:39:58,933] [pool-1-thread-9] Initializing /data/public/NIH/newsirp_final_XML.nii: [testng] 07:39:58,934 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 07:39:58,934 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:39:58,935 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-21_07-39-58.log] [testng] 07:39:58,935 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e724045 - End of configuration. [testng] [2024-03-21 07:39:58,990] [pool-1-thread-8] Initializing /data/public/NIH/minimal.nii: [testng] 07:39:58,991 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 07:39:58,991 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:39:58,991 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-21_07-39-58.log] [testng] 07:39:58,992 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33298cd8 - End of configuration. [testng] [2024-03-21 07:39:59,038] [pool-1-thread-7] Initializing /data/public/NIH/avg152T1_RL_nifti.hdr: [testng] 07:39:59,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 07:39:59,039 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:39:59,040 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-21_07-39-59.log] [testng] 07:39:59,041 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7eec7a4b - End of configuration. [testng] [2024-03-21 07:39:59,079] [pool-1-thread-6] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_26_conf_91.hdr: [testng] 07:39:59,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 07:39:59,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:39:59,081 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-21_07-39-59.log] [testng] 07:39:59,081 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b0c5afb - End of configuration. [testng] [2024-03-21 07:39:59,121] [pool-1-thread-5] Initializing /data/public/NIH/zstat1.nii: [testng] 07:39:59,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 07:39:59,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:39:59,122 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-21_07-39-59.log] [testng] 07:39:59,122 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2147e37e - End of configuration. [testng] [2024-03-21 07:39:59,149] [pool-1-thread-4] Initializing /data/public/NIH/filtered_func_data.nii.gz: [testng] 07:39:59,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 07:39:59,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:39:59,150 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-21_07-39-59.log] [testng] 07:39:59,151 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d39b66d - End of configuration. [testng] [2024-03-21 07:40:02,154] [pool-1-thread-3] Initializing /data/public/NIH/filtered_func_data.nii: [testng] 07:40:02,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 07:40:02,155 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:40:02,156 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-21_07-40-02.log] [testng] 07:40:02,157 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35ce9a97 - End of configuration. [testng] [2024-03-21 07:40:02,190] [pool-1-thread-2] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_94.hdr: [testng] 07:40:02,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 07:40:02,190 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:40:02,191 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-21_07-40-02.log] [testng] 07:40:02,192 |-INFO in ch.qos.logback.core.sift.SiftProcessor@516639ac - End of configuration. [testng] [2024-03-21 07:40:04,349] [pool-1-thread-8] Initializing /data/public/NIH/avg152T1_LR_nifti.nii: [testng] [2024-03-21 07:40:04,395] [pool-1-thread-3] Initializing /data/public/NIH/avg152T1_RL_nifti.nii: [testng] [2024-03-21 07:40:04,441] [pool-1-thread-9] Initializing /data/public/NIH/avg152T1_RL_nifti.nii.gz: [testng] [2024-03-21 07:40:04,777] [pool-1-thread-7] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_100.hdr: [testng] [2024-03-21 07:40:04,806] [pool-1-thread-1] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_100.hdr: [testng] [2024-03-21 07:40:04,847] [pool-1-thread-12] Initializing /data/public/NIH/zstat1.nii.gz: [testng] [2024-03-21 07:40:05,037] [pool-1-thread-6] Initializing /data/public/NIH/minimal.hdr: [testng] [2024-03-21 07:40:05,065] [pool-1-thread-2] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_94.hdr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1060, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 46 seconds Finished: SUCCESS