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Started by upstream project "BIOFORMATS-test-repo" build number 132 originally caused by: Started by upstream project "Trigger" build number 152 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins15158737764548329699.sh + '[' nifti = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_20786_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 12:15:01,721 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 12:15:01,722 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 12:15:01,722 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:15:01,723 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:15:01,723 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 12:15:01,724 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 12:15:01,724 |-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] 12:15:01,724 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:15:01,725 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:15:01,725 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 12:15:01,726 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 12:15:01,726 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 12:15:01,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 12:15:01,913 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 12:15:01,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 12:15:01,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 12:15:01,947 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 12:15:01,948 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 12:15:01,948 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 12:15:01,948 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 12:15:01,948 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 12:15:01,949 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 12:15:01,949 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 224 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-25 12:15:01,959] [main] java.version = 21 [testng] 12:15:01,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 12:15:01,962 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:15:02,007 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-25_12-15-01.log] [testng] 12:15:02,009 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-07-25 12:15:02,011] [main] testng.directory = /data [testng] [2024-07-25 12:15:02,011] [main] testng.configDirectory = /config [testng] [2024-07-25 12:15:02,021] [main] testng.multiplier = 1.0 [testng] [2024-07-25 12:15:02,022] [main] testng.in-memory = false [testng] [2024-07-25 12:15:02,022] [main] testng.allow-missing = false [testng] [2024-07-25 12:15:02,022] [main] user.language = en [testng] [2024-07-25 12:15:02,022] [main] user.country = ${user.country} [testng] [2024-07-25 12:15:02,022] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-25 12:15:02,946] [main] ---------------------------------------- [testng] [2024-07-25 12:15:02,946] [main] Total files: 23 [testng] [2024-07-25 12:15:02,946] [main] Scan time: 0.923 s (40 ms/file) [testng] [2024-07-25 12:15:02,946] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-25 12:15:07,399] [pool-1-thread-1] Initializing /data/public/NIH/avg152T1_LR_nifti.hdr: [testng] 12:15:07,400 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 12:15:07,400 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:15:07,401 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-25_12-15-07.log] [testng] 12:15:07,401 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c58f674 - End of configuration. [testng] [2024-07-25 12:15:07,422] [pool-1-thread-12] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_27_conf_86.hdr: [testng] 12:15:07,422 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 12:15:07,422 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:15:07,423 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-25_12-15-07.log] [testng] 12:15:07,430 |-INFO in ch.qos.logback.core.sift.SiftProcessor@188a9798 - End of configuration. [testng] [2024-07-25 12:15:07,445] [pool-1-thread-11] Initializing /data/qa-17334/volume4d.nii: [testng] 12:15:07,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 12:15:07,445 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:15:07,446 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-25_12-15-07.log] [testng] 12:15:07,447 |-INFO in ch.qos.logback.core.sift.SiftProcessor@137ea0c3 - End of configuration. [testng] [2024-07-25 12:15:07,478] [pool-1-thread-10] Initializing /data/public/NIH/avg152T1_LR_nifti.nii.gz: [testng] 12:15:07,478 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 12:15:07,478 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:15:07,479 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-25_12-15-07.log] [testng] 12:15:07,479 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3265e8c6 - End of configuration. [testng] [2024-07-25 12:15:07,698] [pool-1-thread-9] Initializing /data/public/NIH/newsirp_final_XML.nii: [testng] 12:15:07,698 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 12:15:07,698 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:15:07,698 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-25_12-15-07.log] [testng] 12:15:07,699 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6292a096 - End of configuration. [testng] [2024-07-25 12:15:07,718] [pool-1-thread-8] Initializing /data/public/NIH/minimal.nii: [testng] 12:15:07,718 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 12:15:07,718 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:15:07,719 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-25_12-15-07.log] [testng] 12:15:07,719 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28a44680 - End of configuration. [testng] [2024-07-25 12:15:07,731] [pool-1-thread-7] Initializing /data/public/NIH/avg152T1_RL_nifti.hdr: [testng] 12:15:07,731 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 12:15:07,731 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:15:07,738 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-25_12-15-07.log] [testng] 12:15:07,739 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e6d09d5 - End of configuration. [testng] [2024-07-25 12:15:07,749] [pool-1-thread-6] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_26_conf_91.hdr: [testng] 12:15:07,749 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 12:15:07,749 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:15:07,750 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-25_12-15-07.log] [testng] 12:15:07,750 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14fbb192 - End of configuration. [testng] [2024-07-25 12:15:07,761] [pool-1-thread-5] Initializing /data/public/NIH/zstat1.nii: [testng] 12:15:07,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 12:15:07,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:15:07,761 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-25_12-15-07.log] [testng] 12:15:07,762 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1129a9c5 - End of configuration. [testng] [2024-07-25 12:15:07,774] [pool-1-thread-4] Initializing /data/public/NIH/filtered_func_data.nii.gz: [testng] 12:15:07,774 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 12:15:07,774 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:15:07,775 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-25_12-15-07.log] [testng] 12:15:07,775 |-INFO in ch.qos.logback.core.sift.SiftProcessor@453e2ce0 - End of configuration. [testng] [2024-07-25 12:15:10,471] [pool-1-thread-3] Initializing /data/public/NIH/filtered_func_data.nii: [testng] 12:15:10,471 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 12:15:10,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:15:10,472 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-25_12-15-10.log] [testng] 12:15:10,473 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a2b37c5 - End of configuration. [testng] [2024-07-25 12:15:10,490] [pool-1-thread-2] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_94.hdr: [testng] 12:15:10,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 12:15:10,490 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:15:10,491 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-25_12-15-10.log] [testng] 12:15:10,491 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19c27a86 - End of configuration. [testng] [2024-07-25 12:15:11,951] [pool-1-thread-8] Initializing /data/public/NIH/avg152T1_LR_nifti.nii: [testng] [2024-07-25 12:15:11,975] [pool-1-thread-1] Initializing /data/public/NIH/avg152T1_RL_nifti.nii: [testng] [2024-07-25 12:15:11,991] [pool-1-thread-3] Initializing /data/public/NIH/avg152T1_RL_nifti.nii.gz: [testng] [2024-07-25 12:15:12,193] [pool-1-thread-9] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_100.hdr: [testng] [2024-07-25 12:15:12,202] [pool-1-thread-6] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_100.hdr: [testng] [2024-07-25 12:15:12,212] [pool-1-thread-12] Initializing /data/public/NIH/zstat1.nii.gz: [testng] [2024-07-25 12:15:12,277] [pool-1-thread-2] Initializing /data/public/NIH/minimal.hdr: [testng] [2024-07-25 12:15:12,286] [pool-1-thread-11] 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: 38 seconds Finished: SUCCESS