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Started by upstream project "BIOFORMATS-test-repo" build number 273 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins17368688669737401491.sh + '[' analyze = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_43072_merge_ci -v /uod/idr/repos/curated/analyze:/data -v /uod/idr-scratch/merge-ci/curated/analyze:/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 test-automated: [testng] File leak detector installed [testng] 10:05:38,541 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 10:05:38,542 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 10:05:38,542 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:05:38,543 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 10:05:38,544 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 10:05:38,544 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 10:05:38,544 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 10:05:38,544 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:05:38,544 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 10:05:38,545 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 10:05:38,545 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 10:05:38,545 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 10:05:38,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 10:05:38,759 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 10:05:38,786 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 10:05:38,786 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 10:05:38,793 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 10:05:38,793 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 10:05:38,793 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 10:05:38,794 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 10:05:38,794 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 10:05:38,795 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 10:05:38,795 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 251 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-29 10:05:38,804] [main] java.version = 1.8.0_342 [testng] 10:05:38,807 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 10:05:38,808 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:05:38,851 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-29_10-05-38.log] [testng] 10:05:38,852 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-29 10:05:38,854] [main] testng.directory = /data [testng] [2024-11-29 10:05:38,854] [main] testng.configDirectory = /config [testng] [2024-11-29 10:05:38,865] [main] testng.multiplier = 1.0 [testng] [2024-11-29 10:05:38,866] [main] testng.in-memory = false [testng] [2024-11-29 10:05:38,866] [main] testng.allow-missing = false [testng] [2024-11-29 10:05:38,866] [main] user.language = en [testng] [2024-11-29 10:05:38,866] [main] user.country = ${user.country} [testng] [2024-11-29 10:05:38,866] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-29 10:05:54,775] [main] ---------------------------------------- [testng] [2024-11-29 10:05:54,775] [main] Total files: 21 [testng] [2024-11-29 10:05:54,775] [main] Scan time: 15.909 s (757 ms/file) [testng] [2024-11-29 10:05:54,775] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-29 10:06:13,246] [pool-1-thread-1] Initializing /data/frans/m000-MR_CHEST.gif: [testng] 10:06:13,247 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 10:06:13,247 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:06:13,248 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-29_10-06-13.log] [testng] 10:06:13,248 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e79dfa9 - End of configuration. [testng] [2024-11-29 10:06:13,502] [pool-1-thread-12] Initializing /data/frans/betmask.hdr: [testng] 10:06:13,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 10:06:13,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:06:13,503 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-29_10-06-13.log] [testng] 10:06:13,503 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39c167d9 - End of configuration. [testng] [2024-11-29 10:06:14,394] [pool-1-thread-11] Initializing /data/frans/Test Files for Frans/PLA-zm2-16mm_1002_MF_V1.hdr: [testng] 10:06:14,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 10:06:14,395 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:06:14,395 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-29_10-06-14.log] [testng] 10:06:14,396 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d2cc31f - End of configuration. [testng] [2024-11-29 10:06:15,200] [pool-1-thread-10] Initializing /data/frans/MR_SEGBRAIN.hdr: [testng] 10:06:15,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 10:06:15,200 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:06:15,201 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-29_10-06-15.log] [testng] 10:06:15,201 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e5071e7 - End of configuration. [testng] [2024-11-29 10:06:15,949] [pool-1-thread-9] Initializing /data/frans/Test Files for Frans/1002-sag-transform-box-est_flip-ord.hdr: [testng] 10:06:15,949 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 10:06:15,949 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:06:15,949 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-29_10-06-15.log] [testng] 10:06:15,950 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66549e - End of configuration. [testng] [2024-11-29 10:06:16,691] [pool-1-thread-8] Initializing /data/frans/aal.hdr: [testng] 10:06:16,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 10:06:16,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:06:16,692 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-29_10-06-16.log] [testng] 10:06:16,692 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1bf8ea74 - End of configuration. [testng] [2024-11-29 10:06:17,427] [pool-1-thread-7] Initializing /data/frans/CT_KNEE.hdr: [testng] 10:06:17,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 10:06:17,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:06:17,428 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-29_10-06-17.log] [testng] 10:06:17,428 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3916efee - End of configuration. [testng] [2024-11-29 10:06:18,160] [pool-1-thread-6] Initializing /data/frans/MR_CHEST.hdr: [testng] 10:06:18,160 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 10:06:18,160 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:06:18,160 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-29_10-06-18.log] [testng] 10:06:18,161 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22578fc5 - End of configuration. [testng] [2024-11-29 10:06:18,892] [pool-1-thread-5] Initializing /data/frans/CT_CRANI.hdr: [testng] 10:06:18,892 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 10:06:18,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:06:18,893 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-29_10-06-18.log] [testng] 10:06:18,894 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68b0d3d5 - End of configuration. [testng] [2024-11-29 10:06:19,782] [pool-1-thread-4] Initializing /data/frans/ch2.hdr: [testng] 10:06:19,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 10:06:19,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:06:19,782 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-29_10-06-19.log] [testng] 10:06:19,783 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1a1349ad - End of configuration. [testng] [2024-11-29 10:06:20,684] [pool-1-thread-3] Initializing /data/frans/CT_WHOLE.hdr: [testng] 10:06:20,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 10:06:20,685 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:06:20,685 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-29_10-06-20.log] [testng] 10:06:20,686 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27949bae - End of configuration. [testng] [2024-11-29 10:06:21,655] [pool-1-thread-2] Initializing /data/frans/Test Files for Frans/F005_1002_MF_SCAN1_stat_brain_fdg_JJ_Volume_Corrected.hdr: [testng] 10:06:21,655 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 10:06:21,655 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:06:21,656 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-29_10-06-21.log] [testng] 10:06:21,656 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59149c41 - End of configuration. [testng] [2024-11-29 10:06:26,086] [pool-1-thread-1] Initializing /data/frans/CT_FOOT.hdr: [testng] [2024-11-29 10:06:32,965] [pool-1-thread-12] Initializing /data/frans/CT_CHEST.hdr: [testng] [2024-11-29 10:06:33,823] [pool-1-thread-11] Initializing /data/frans/brodmann.hdr: [testng] [2024-11-29 10:06:34,745] [pool-1-thread-2] Initializing /data/frans/Test Files for Frans/06-101-mask-40pc2dil.hdr: [testng] [2024-11-29 10:06:35,788] [pool-1-thread-10] Initializing /data/frans/Test Files for Frans/200-PLA_sansBD_spmT_0005.hdr: [testng] [2024-11-29 10:06:36,777] [pool-1-thread-5] Initializing /data/frans/ch2bet.hdr: [testng] [2024-11-29 10:06:37,737] [pool-1-thread-9] Initializing /data/frans/CT_HAND.hdr: [testng] [2024-11-29 10:06:38,690] [pool-1-thread-7] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1.img.hdr: [testng] [2024-11-29 10:06:39,886] [pool-1-thread-4] Initializing /data/frans/CT_APERT.hdr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1113, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 1 minute 13 seconds Finished: SUCCESS