Started by upstream project "BIOFORMATS-test-repo" build number 299 originally caused by: Started by upstream project "Trigger" build number 321 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/jenkins7700276634713979499.sh + '[' nifti = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_47382_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 05:35:55,505 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 05:35:55,506 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 05:35:55,506 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:35:55,507 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:35:55,508 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 05:35:55,508 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 05:35:55,509 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 05:35:55,509 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:35:55,509 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:35:55,510 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 05:35:55,510 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 05:35:55,510 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 05:35:55,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 05:35:55,678 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 05:35:55,705 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 05:35:55,705 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 05:35:55,712 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 05:35:55,712 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 05:35:55,712 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 05:35:55,713 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 05:35:55,713 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 05:35:55,714 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 05:35:55,714 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 205 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-26 05:35:55,724] [main] java.version = 21 [testng] 05:35:55,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:35:55,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:35:55,772 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-26_05-35-55.log] [testng] 05:35:55,774 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-12-26 05:35:55,775] [main] testng.directory = /data [testng] [2024-12-26 05:35:55,776] [main] testng.configDirectory = /config [testng] [2024-12-26 05:35:55,790] [main] testng.multiplier = 1.0 [testng] [2024-12-26 05:35:55,791] [main] testng.in-memory = false [testng] [2024-12-26 05:35:55,791] [main] testng.allow-missing = false [testng] [2024-12-26 05:35:55,791] [main] user.language = en [testng] [2024-12-26 05:35:55,791] [main] user.country = ${user.country} [testng] [2024-12-26 05:35:55,791] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-26 05:36:19,570] [main] ---------------------------------------- [testng] [2024-12-26 05:36:19,570] [main] Total files: 23 [testng] [2024-12-26 05:36:19,570] [main] Scan time: 23.779 s (1033 ms/file) [testng] [2024-12-26 05:36:19,571] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-26 05:37:15,829] [pool-1-thread-1] Initializing /data/public/NIH/avg152T1_RL_nifti.nii.gz: [testng] 05:37:15,830 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 05:37:15,830 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:37:15,832 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-26_05-37-15.log] [testng] 05:37:15,832 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e2cad15 - End of configuration. [testng] [2024-12-26 05:37:21,660] [pool-1-thread-12] Initializing /data/public/NIH/avg152T1_LR_nifti.nii.gz: [testng] 05:37:21,660 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 05:37:21,660 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:37:21,661 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-26_05-37-21.log] [testng] 05:37:21,661 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a1b13fb - End of configuration. [testng] [2024-12-26 05:37:27,431] [pool-1-thread-11] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_100.hdr: [testng] 05:37:27,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 05:37:27,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:37:27,432 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-26_05-37-27.log] [testng] 05:37:27,433 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5adad8c1 - End of configuration. [testng] [2024-12-26 05:37:28,883] [pool-1-thread-10] Initializing /data/public/NIH/filtered_func_data.nii.gz: [testng] 05:37:28,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 05:37:28,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:37:28,884 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-26_05-37-28.log] [testng] 05:37:28,884 |-INFO in ch.qos.logback.core.sift.SiftProcessor@236ab365 - End of configuration. [testng] [2024-12-26 05:37:37,082] [pool-1-thread-9] Initializing /data/public/NIH/minimal.hdr: [testng] 05:37:37,082 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 05:37:37,082 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:37:37,083 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-26_05-37-37.log] [testng] 05:37:37,084 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c3fdfa4 - End of configuration. [testng] [2024-12-26 05:37:38,384] [pool-1-thread-8] Initializing /data/public/NIH/avg152T1_LR_nifti.nii: [testng] 05:37:38,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 05:37:38,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:37:38,385 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-26_05-37-38.log] [testng] 05:37:38,385 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50b02226 - End of configuration. [testng] [2024-12-26 05:37:39,646] [pool-1-thread-7] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_27_conf_86.hdr: [testng] 05:37:39,646 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 05:37:39,646 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:37:39,647 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-26_05-37-39.log] [testng] 05:37:39,647 |-INFO in ch.qos.logback.core.sift.SiftProcessor@320c2eee - End of configuration. [testng] [2024-12-26 05:37:40,991] [pool-1-thread-6] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_94.hdr: [testng] 05:37:40,991 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 05:37:40,992 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:37:40,992 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-26_05-37-40.log] [testng] 05:37:40,993 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67d2ac7c - End of configuration. [testng] [2024-12-26 05:37:42,317] [pool-1-thread-5] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_26_conf_91.hdr: [testng] 05:37:42,317 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 05:37:42,317 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:37:42,318 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-26_05-37-42.log] [testng] 05:37:42,318 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75421e38 - End of configuration. [testng] [2024-12-26 05:37:43,618] [pool-1-thread-4] Initializing /data/public/NIH/zstat1.nii.gz: [testng] 05:37:43,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 05:37:43,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:37:43,619 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-26_05-37-43.log] [testng] 05:37:43,619 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5af212d8 - End of configuration. [testng] [2024-12-26 05:37:48,814] [pool-1-thread-3] Initializing /data/public/NIH/zstat1.nii: [testng] 05:37:48,815 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 05:37:48,815 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:37:48,815 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-26_05-37-48.log] [testng] 05:37:48,816 |-INFO in ch.qos.logback.core.sift.SiftProcessor@adc73a1 - End of configuration. [testng] [2024-12-26 05:37:50,041] [pool-1-thread-2] Initializing /data/public/NIH/avg152T1_RL_nifti.nii: [testng] 05:37:50,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 05:37:50,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:37:50,042 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-26_05-37-50.log] [testng] 05:37:50,042 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ee1059b - End of configuration. [testng] [2024-12-26 05:38:00,930] [pool-1-thread-2] Initializing /data/public/NIH/filtered_func_data.nii: [testng] [2024-12-26 05:38:02,265] [pool-1-thread-3] Initializing /data/qa-17334/volume4d.nii: [testng] [2024-12-26 05:38:03,609] [pool-1-thread-8] Initializing /data/public/NIH/avg152T1_LR_nifti.hdr: [testng] [2024-12-26 05:38:08,990] [pool-1-thread-6] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_94.hdr: [testng] [2024-12-26 05:38:10,481] [pool-1-thread-7] Initializing /data/public/NIH/minimal.nii: [testng] [2024-12-26 05:38:11,758] [pool-1-thread-11] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_100.hdr: [testng] [2024-12-26 05:38:13,135] [pool-1-thread-5] Initializing /data/public/NIH/newsirp_final_XML.nii: [testng] [2024-12-26 05:38:14,354] [pool-1-thread-9] Initializing /data/public/NIH/avg152T1_RL_nifti.hdr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1060, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 3 minutes 1 second Finished: SUCCESS