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Started by upstream project "BIOFORMATS-test-repo" build number 294 originally caused by: Started by upstream project "Trigger" build number 313 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins7740256645504231029.sh + '[' nifti = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_46556_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] 1 warning 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] 14:56:16,811 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 14:56:16,812 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 14:56:16,812 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 14:56:16,813 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 14:56:16,813 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 14:56:16,813 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 14:56:16,814 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 14:56:16,814 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 14:56:16,814 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 14:56:16,815 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 14:56:16,815 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 14:56:16,815 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 14:56:16,978 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 14:56:16,978 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 14:56:17,000 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 14:56:17,000 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 14:56:17,006 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 14:56:17,006 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 14:56:17,006 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 14:56:17,006 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 14:56:17,006 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 14:56:17,007 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 14:56:17,007 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 193 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-18 14:56:17,017] [main] java.version = 17.0.2 [testng] 14:56:17,020 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 14:56:17,020 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:56:17,061 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-18_14-56-17.log] [testng] 14:56:17,063 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-12-18 14:56:17,065] [main] testng.directory = /data [testng] [2024-12-18 14:56:17,065] [main] testng.configDirectory = /config [testng] [2024-12-18 14:56:17,073] [main] testng.multiplier = 1.0 [testng] [2024-12-18 14:56:17,074] [main] testng.in-memory = false [testng] [2024-12-18 14:56:17,074] [main] testng.allow-missing = false [testng] [2024-12-18 14:56:17,074] [main] user.language = en [testng] [2024-12-18 14:56:17,074] [main] user.country = ${user.country} [testng] [2024-12-18 14:56:17,074] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-18 15:01:19,111] [main] ---------------------------------------- [testng] [2024-12-18 15:01:19,111] [main] Total files: 23 [testng] [2024-12-18 15:01:19,112] [main] Scan time: 302.037 s (13132 ms/file) [testng] [2024-12-18 15:01:19,112] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-18 15:08:26,310] [pool-1-thread-1] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_94.hdr: [testng] 15:08:26,310 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 15:08:26,310 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:08:26,311 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-18_15-08-26.log] [testng] 15:08:26,312 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d5421e1 - End of configuration. [testng] [2024-12-18 15:08:42,771] [pool-1-thread-12] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_100.hdr: [testng] 15:08:42,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 15:08:42,771 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:08:42,772 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-18_15-08-42.log] [testng] 15:08:42,772 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26f94642 - End of configuration. [testng] [2024-12-18 15:08:59,169] [pool-1-thread-11] Initializing /data/public/NIH/minimal.nii: [testng] 15:08:59,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 15:08:59,170 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:08:59,170 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-18_15-08-59.log] [testng] 15:08:59,171 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17b2dc67 - End of configuration. [testng] [2024-12-18 15:09:14,612] [pool-1-thread-10] Initializing /data/qa-17334/volume4d.nii: [testng] 15:09:14,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 15:09:14,613 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:09:14,613 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-18_15-09-14.log] [testng] 15:09:14,614 |-INFO in ch.qos.logback.core.sift.SiftProcessor@769ecc81 - End of configuration. [testng] [2024-12-18 15:09:29,906] [pool-1-thread-9] Initializing /data/public/NIH/zstat1.nii: [testng] 15:09:29,906 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 15:09:29,906 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:09:29,907 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-18_15-09-29.log] [testng] 15:09:29,907 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27d492c3 - End of configuration. [testng] [2024-12-18 15:09:46,516] [pool-1-thread-8] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_28_conf_94.hdr: [testng] 15:09:46,516 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 15:09:46,516 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:09:46,517 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-18_15-09-46.log] [testng] 15:09:46,517 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a3650b6 - End of configuration. [testng] [2024-12-18 15:10:04,819] [pool-1-thread-7] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_26_conf_91.hdr: [testng] 15:10:04,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 15:10:04,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:10:04,820 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-18_15-10-04.log] [testng] 15:10:04,821 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d5fed2e - End of configuration. [testng] [2024-12-18 15:10:21,680] [pool-1-thread-6] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_25_conf_100.hdr: [testng] 15:10:21,680 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 15:10:21,680 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:10:21,681 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-18_15-10-21.log] [testng] 15:10:21,681 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1869528d - End of configuration. [testng] [2024-12-18 15:10:39,255] [pool-1-thread-5] Initializing /data/public/NIH/avg152T1_RL_nifti.hdr: [testng] 15:10:39,256 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 15:10:39,256 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:10:39,256 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-18_15-10-39.log] [testng] 15:10:39,257 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7aede80f - End of configuration. [testng] [2024-12-18 15:10:54,223] [pool-1-thread-4] Initializing /data/public/NIH/avg152T1_LR_nifti.nii: [testng] 15:10:54,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 15:10:54,223 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:10:54,224 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-18_15-10-54.log] [testng] 15:10:54,224 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50e857fd - End of configuration. [testng] [2024-12-18 15:11:01,580] [pool-1-thread-3] Initializing /data/public/NIH/avg152T1_LR_nifti.hdr: [testng] 15:11:01,580 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 15:11:01,580 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:11:01,581 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-18_15-11-01.log] [testng] 15:11:01,581 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ef7ee08 - End of configuration. [testng] [2024-12-18 15:11:11,451] [pool-1-thread-2] Initializing /data/public/NIH/filtered_func_data.nii.gz: [testng] 15:11:11,451 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 15:11:11,451 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:11:11,452 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-18_15-11-11.log] [testng] 15:11:11,452 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6091627b - End of configuration. [testng] [2024-12-18 15:12:36,204] [pool-1-thread-11] Initializing /data/public/NIH/minimal.hdr: [testng] [2024-12-18 15:12:43,773] [pool-1-thread-4] Initializing /data/public/NIH/newsirp_final_XML.nii: [testng] [2024-12-18 15:12:53,799] [pool-1-thread-9] Initializing /data/public/NIH/avg152T1_RL_nifti.nii: [testng] [2024-12-18 15:12:57,151] [pool-1-thread-10] Initializing /data/public/NIH/zstat1.nii.gz: [testng] [2024-12-18 15:13:33,051] [pool-1-thread-5] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1_rat_27_conf_86.hdr: [testng] [2024-12-18 15:13:40,192] [pool-1-thread-6] Initializing /data/public/NIH/avg152T1_RL_nifti.nii.gz: [testng] [2024-12-18 15:14:08,106] [pool-1-thread-3] Initializing /data/public/NIH/avg152T1_LR_nifti.nii.gz: [testng] [2024-12-18 15:14:29,466] [pool-1-thread-12] Initializing /data/public/NIH/filtered_func_data.nii: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1060, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 20 minutes 3 seconds Finished: SUCCESS