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Started by upstream project "BIOFORMATS-test-repo" build number 249 originally caused by: Started by upstream project "Trigger" build number 273 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins10441367104383528745.sh + '[' analyze = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_39265_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] 03:45:06,905 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:45:06,907 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 03:45:06,907 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:45:06,908 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:45:06,908 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:45:06,908 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:45:06,908 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 03:45:06,908 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:45:06,909 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:45:06,909 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:45:06,909 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:45:06,909 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:45:07,130 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:45:07,130 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:45:07,157 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:45:07,157 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:45:07,165 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:45:07,165 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:45:07,165 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:45:07,165 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:45:07,166 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 03:45:07,166 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 03:45:07,166 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 257 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-08 03:45:07,176] [main] java.version = 1.8.0_342 [testng] 03:45:07,179 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:45:07,179 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:07,223 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-08_03-45-07.log] [testng] 03:45:07,224 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-08 03:45:07,226] [main] testng.directory = /data [testng] [2024-11-08 03:45:07,226] [main] testng.configDirectory = /config [testng] [2024-11-08 03:45:07,238] [main] testng.multiplier = 1.0 [testng] [2024-11-08 03:45:07,238] [main] testng.in-memory = false [testng] [2024-11-08 03:45:07,238] [main] testng.allow-missing = false [testng] [2024-11-08 03:45:07,238] [main] user.language = en [testng] [2024-11-08 03:45:07,238] [main] user.country = ${user.country} [testng] [2024-11-08 03:45:07,238] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-08 03:45:13,333] [main] ---------------------------------------- [testng] [2024-11-08 03:45:13,334] [main] Total files: 21 [testng] [2024-11-08 03:45:13,334] [main] Scan time: 6.094 s (290 ms/file) [testng] [2024-11-08 03:45:13,334] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-08 03:45:20,443] [pool-1-thread-1] Initializing /data/frans/m000-MR_CHEST.gif: [testng] 03:45:20,443 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:45:20,443 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:20,444 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-08_03-45-20.log] [testng] 03:45:20,445 |-INFO in ch.qos.logback.core.sift.SiftProcessor@82b851c - End of configuration. [testng] [2024-11-08 03:45:20,549] [pool-1-thread-12] Initializing /data/frans/betmask.hdr: [testng] 03:45:20,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:45:20,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:20,550 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-08_03-45-20.log] [testng] 03:45:20,550 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d3ce98b - End of configuration. [testng] [2024-11-08 03:45:20,831] [pool-1-thread-11] Initializing /data/frans/Test Files for Frans/PLA-zm2-16mm_1002_MF_V1.hdr: [testng] 03:45:20,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:45:20,831 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:20,832 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-08_03-45-20.log] [testng] 03:45:20,832 |-INFO in ch.qos.logback.core.sift.SiftProcessor@477f3814 - End of configuration. [testng] [2024-11-08 03:45:21,106] [pool-1-thread-10] Initializing /data/frans/MR_SEGBRAIN.hdr: [testng] 03:45:21,106 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:45:21,106 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:21,107 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-08_03-45-21.log] [testng] 03:45:21,107 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d4acaa4 - End of configuration. [testng] [2024-11-08 03:45:21,390] [pool-1-thread-9] Initializing /data/frans/Test Files for Frans/1002-sag-transform-box-est_flip-ord.hdr: [testng] 03:45:21,390 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:45:21,390 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:21,391 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-08_03-45-21.log] [testng] 03:45:21,391 |-INFO in ch.qos.logback.core.sift.SiftProcessor@205ca225 - End of configuration. [testng] [2024-11-08 03:45:21,673] [pool-1-thread-8] Initializing /data/frans/aal.hdr: [testng] 03:45:21,674 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:45:21,674 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:21,674 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-08_03-45-21.log] [testng] 03:45:21,674 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3fe5826 - End of configuration. [testng] [2024-11-08 03:45:21,965] [pool-1-thread-7] Initializing /data/frans/CT_KNEE.hdr: [testng] 03:45:21,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:45:21,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:21,965 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-08_03-45-21.log] [testng] 03:45:21,966 |-INFO in ch.qos.logback.core.sift.SiftProcessor@777111c7 - End of configuration. [testng] [2024-11-08 03:45:22,256] [pool-1-thread-6] Initializing /data/frans/MR_CHEST.hdr: [testng] 03:45:22,256 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:45:22,256 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:22,257 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-08_03-45-22.log] [testng] 03:45:22,257 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33526587 - End of configuration. [testng] [2024-11-08 03:45:22,533] [pool-1-thread-5] Initializing /data/frans/CT_CRANI.hdr: [testng] 03:45:22,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:45:22,533 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:22,533 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-08_03-45-22.log] [testng] 03:45:22,534 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34ca757f - End of configuration. [testng] [2024-11-08 03:45:22,813] [pool-1-thread-4] Initializing /data/frans/ch2.hdr: [testng] 03:45:22,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:45:22,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:22,813 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-08_03-45-22.log] [testng] 03:45:22,814 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20874e48 - End of configuration. [testng] [2024-11-08 03:45:23,089] [pool-1-thread-3] Initializing /data/frans/CT_WHOLE.hdr: [testng] 03:45:23,089 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:45:23,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:23,090 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-08_03-45-23.log] [testng] 03:45:23,091 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e91038d - End of configuration. [testng] [2024-11-08 03:45:23,402] [pool-1-thread-2] Initializing /data/frans/Test Files for Frans/F005_1002_MF_SCAN1_stat_brain_fdg_JJ_Volume_Corrected.hdr: [testng] 03:45:23,402 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:45:23,402 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:45:23,403 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-08_03-45-23.log] [testng] 03:45:23,403 |-INFO in ch.qos.logback.core.sift.SiftProcessor@274d977d - End of configuration. [testng] [2024-11-08 03:45:26,044] [pool-1-thread-1] Initializing /data/frans/CT_FOOT.hdr: [testng] [2024-11-08 03:45:29,182] [pool-1-thread-12] Initializing /data/frans/CT_CHEST.hdr: [testng] [2024-11-08 03:45:29,455] [pool-1-thread-11] Initializing /data/frans/brodmann.hdr: [testng] [2024-11-08 03:45:29,749] [pool-1-thread-2] Initializing /data/frans/Test Files for Frans/06-101-mask-40pc2dil.hdr: [testng] [2024-11-08 03:45:30,044] [pool-1-thread-4] Initializing /data/frans/ch2bet.hdr: [testng] [2024-11-08 03:45:30,320] [pool-1-thread-3] Initializing /data/frans/CT_HAND.hdr: [testng] [2024-11-08 03:45:30,599] [pool-1-thread-6] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1.img.hdr: [testng] [2024-11-08 03:45:30,882] [pool-1-thread-5] Initializing /data/frans/CT_APERT.hdr: [testng] [2024-11-08 03:45:31,152] [pool-1-thread-7] Initializing /data/frans/Test Files for Frans/200-PLA_sansBD_spmT_0005.hdr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1113, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 33 seconds Finished: SUCCESS