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Started by upstream project "BIOFORMATS-test-repo" build number 217 originally caused by: Started by upstream project "Trigger" build number 244 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@10 [BIOFORMATS-test-folder@10] $ /bin/bash -xe /tmp/jenkins16901287888717785261.sh + '[' analyze = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_34480_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] 06:56:49,195 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 06:56:49,196 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 06:56:49,196 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:56:49,197 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 06:56:49,197 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 06:56:49,198 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 06:56:49,198 |-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] 06:56:49,198 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:56:49,198 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 06:56:49,199 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 06:56:49,199 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 06:56:49,199 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 06:56:49,409 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 06:56:49,409 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 06:56:49,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 06:56:49,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 06:56:49,441 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 06:56:49,442 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 06:56:49,442 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 06:56:49,442 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 06:56:49,442 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 06:56:49,443 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 06:56:49,443 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 245 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-11 06:56:49,453] [main] java.version = 1.8.0_342 [testng] 06:56:49,456 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 06:56:49,456 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:56:49,500 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-11_06-56-49.log] [testng] 06:56:49,502 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-10-11 06:56:49,503] [main] testng.directory = /data [testng] [2024-10-11 06:56:49,504] [main] testng.configDirectory = /config [testng] [2024-10-11 06:56:49,515] [main] testng.multiplier = 1.0 [testng] [2024-10-11 06:56:49,516] [main] testng.in-memory = false [testng] [2024-10-11 06:56:49,516] [main] testng.allow-missing = false [testng] [2024-10-11 06:56:49,516] [main] user.language = en [testng] [2024-10-11 06:56:49,516] [main] user.country = ${user.country} [testng] [2024-10-11 06:56:49,516] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-11 06:57:04,862] [main] ---------------------------------------- [testng] [2024-10-11 06:57:04,862] [main] Total files: 21 [testng] [2024-10-11 06:57:04,862] [main] Scan time: 15.346 s (730 ms/file) [testng] [2024-10-11 06:57:04,862] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-11 06:57:21,999] [pool-1-thread-1] Initializing /data/frans/m000-MR_CHEST.gif: [testng] 06:57:21,999 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 06:57:22,000 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:57:22,001 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-11_06-57-22.log] [testng] 06:57:22,001 |-INFO in ch.qos.logback.core.sift.SiftProcessor@65ec8743 - End of configuration. [testng] [2024-10-11 06:57:22,195] [pool-1-thread-12] Initializing /data/frans/betmask.hdr: [testng] 06:57:22,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 06:57:22,196 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:57:22,196 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-11_06-57-22.log] [testng] 06:57:22,197 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d7743f5 - End of configuration. [testng] [2024-10-11 06:57:22,777] [pool-1-thread-11] Initializing /data/frans/Test Files for Frans/PLA-zm2-16mm_1002_MF_V1.hdr: [testng] 06:57:22,777 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 06:57:22,777 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:57:22,778 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-11_06-57-22.log] [testng] 06:57:22,778 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a60b573 - End of configuration. [testng] [2024-10-11 06:57:23,878] [pool-1-thread-10] Initializing /data/frans/MR_SEGBRAIN.hdr: [testng] 06:57:23,878 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 06:57:23,879 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:57:23,879 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-11_06-57-23.log] [testng] 06:57:23,880 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c48bf65 - End of configuration. [testng] [2024-10-11 06:57:24,817] [pool-1-thread-9] Initializing /data/frans/Test Files for Frans/1002-sag-transform-box-est_flip-ord.hdr: [testng] 06:57:24,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 06:57:24,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:57:24,818 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-11_06-57-24.log] [testng] 06:57:24,818 |-INFO in ch.qos.logback.core.sift.SiftProcessor@521fd43d - End of configuration. [testng] [2024-10-11 06:57:25,378] [pool-1-thread-8] Initializing /data/frans/aal.hdr: [testng] 06:57:25,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 06:57:25,378 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:57:25,379 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-11_06-57-25.log] [testng] 06:57:25,379 |-INFO in ch.qos.logback.core.sift.SiftProcessor@641adf66 - End of configuration. [testng] [2024-10-11 06:57:26,238] [pool-1-thread-7] Initializing /data/frans/CT_KNEE.hdr: [testng] 06:57:26,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 06:57:26,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:57:26,239 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-11_06-57-26.log] [testng] 06:57:26,239 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4329f73 - End of configuration. [testng] [2024-10-11 06:57:27,076] [pool-1-thread-6] Initializing /data/frans/MR_CHEST.hdr: [testng] 06:57:27,076 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 06:57:27,076 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:57:27,077 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-11_06-57-27.log] [testng] 06:57:27,077 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ced025d - End of configuration. [testng] [2024-10-11 06:57:27,658] [pool-1-thread-5] Initializing /data/frans/CT_CRANI.hdr: [testng] 06:57:27,658 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 06:57:27,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:57:27,659 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-11_06-57-27.log] [testng] 06:57:27,659 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4775441e - End of configuration. [testng] [2024-10-11 06:57:28,350] [pool-1-thread-4] Initializing /data/frans/ch2.hdr: [testng] 06:57:28,350 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 06:57:28,350 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:57:28,351 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-11_06-57-28.log] [testng] 06:57:28,351 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4aa3fe2a - End of configuration. [testng] [2024-10-11 06:57:29,047] [pool-1-thread-3] Initializing /data/frans/CT_WHOLE.hdr: [testng] 06:57:29,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 06:57:29,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:57:29,048 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-11_06-57-29.log] [testng] 06:57:29,049 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22fcde77 - End of configuration. [testng] [2024-10-11 06:57:29,733] [pool-1-thread-2] Initializing /data/frans/Test Files for Frans/F005_1002_MF_SCAN1_stat_brain_fdg_JJ_Volume_Corrected.hdr: [testng] 06:57:29,733 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 06:57:29,733 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 06:57:29,734 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-11_06-57-29.log] [testng] 06:57:29,734 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1853b49a - End of configuration. [testng] [2024-10-11 06:57:33,537] [pool-1-thread-1] Initializing /data/frans/CT_FOOT.hdr: [testng] [2024-10-11 06:57:39,447] [pool-1-thread-11] Initializing /data/frans/CT_CHEST.hdr: [testng] [2024-10-11 06:57:40,191] [pool-1-thread-5] Initializing /data/frans/ch2bet.hdr: [testng] [2024-10-11 06:57:40,836] [pool-1-thread-6] Initializing /data/frans/CT_HAND.hdr: [testng] [2024-10-11 06:57:41,543] [pool-1-thread-10] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1.img.hdr: [testng] [2024-10-11 06:57:42,207] [pool-1-thread-3] Initializing /data/frans/CT_APERT.hdr: [testng] [2024-10-11 06:57:42,888] [pool-1-thread-7] Initializing /data/frans/Test Files for Frans/200-PLA_sansBD_spmT_0005.hdr: [testng] [2024-10-11 06:57:43,595] [pool-1-thread-12] Initializing /data/frans/brodmann.hdr: [testng] [2024-10-11 06:57:44,429] [pool-1-thread-2] Initializing /data/frans/Test Files for Frans/06-101-mask-40pc2dil.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 6 seconds Finished: SUCCESS