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Started by upstream project "BIOFORMATS-test-repo" build number 266 originally caused by: Started by upstream project "Trigger" build number 289 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins4382677738047933435.sh + '[' analyze = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_42053_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 [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] 03:47:19,176 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:47:19,177 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 03:47:19,177 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:47:19,178 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:47:19,179 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:47:19,179 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:47:19,179 |-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] 03:47:19,179 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:47:19,180 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:47:19,180 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:47:19,180 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:47:19,181 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:47:19,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:47:19,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:47:19,352 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:47:19,353 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:47:19,357 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:47:19,357 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:47:19,357 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:47:19,358 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:47:19,358 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 03:47:19,359 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 03:47:19,359 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 179 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-24 03:47:19,367] [main] java.version = 17.0.2 [testng] 03:47:19,370 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:47:19,370 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:47:19,407 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-24_03-47-19.log] [testng] 03:47:19,408 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-11-24 03:47:19,410] [main] testng.directory = /data [testng] [2024-11-24 03:47:19,410] [main] testng.configDirectory = /config [testng] [2024-11-24 03:47:19,418] [main] testng.multiplier = 1.0 [testng] [2024-11-24 03:47:19,419] [main] testng.in-memory = false [testng] [2024-11-24 03:47:19,419] [main] testng.allow-missing = false [testng] [2024-11-24 03:47:19,419] [main] user.language = en [testng] [2024-11-24 03:47:19,419] [main] user.country = ${user.country} [testng] [2024-11-24 03:47:19,419] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-24 03:47:31,224] [main] ---------------------------------------- [testng] [2024-11-24 03:47:31,224] [main] Total files: 21 [testng] [2024-11-24 03:47:31,224] [main] Scan time: 11.805 s (562 ms/file) [testng] [2024-11-24 03:47:31,224] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-24 03:47:44,656] [pool-1-thread-1] Initializing /data/frans/CT_CRANI.hdr: [testng] 03:47:44,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:47:44,657 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:47:44,658 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-24_03-47-44.log] [testng] 03:47:44,659 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c3dec1f - End of configuration. [testng] [2024-11-24 03:47:45,346] [pool-1-thread-12] Initializing /data/frans/aal.hdr: [testng] 03:47:45,346 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:47:45,346 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:47:45,348 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-24_03-47-45.log] [testng] 03:47:45,348 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7d4323e0 - End of configuration. [testng] [2024-11-24 03:47:46,177] [pool-1-thread-11] Initializing /data/frans/CT_APERT.hdr: [testng] 03:47:46,177 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:47:46,179 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:47:46,181 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-24_03-47-46.log] [testng] 03:47:46,183 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a36e5f8 - End of configuration. [testng] [2024-11-24 03:47:46,902] [pool-1-thread-10] Initializing /data/frans/Test Files for Frans/200-PLA_sansBD_spmT_0005.hdr: [testng] 03:47:46,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:47:46,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:47:46,903 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-24_03-47-46.log] [testng] 03:47:46,903 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b4b98bf - End of configuration. [testng] [2024-11-24 03:47:47,427] [pool-1-thread-9] Initializing /data/frans/CT_CHEST.hdr: [testng] 03:47:47,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:47:47,427 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:47:47,428 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-24_03-47-47.log] [testng] 03:47:47,428 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b4a5e86 - End of configuration. [testng] [2024-11-24 03:47:48,112] [pool-1-thread-8] Initializing /data/frans/ch2bet.hdr: [testng] 03:47:48,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:47:48,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:47:48,113 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-24_03-47-48.log] [testng] 03:47:48,113 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e26dc38 - End of configuration. [testng] [2024-11-24 03:47:48,847] [pool-1-thread-7] Initializing /data/frans/betmask.hdr: [testng] 03:47:48,848 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:47:48,848 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:47:48,848 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-24_03-47-48.log] [testng] 03:47:48,849 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d9de168 - End of configuration. [testng] [2024-11-24 03:47:49,467] [pool-1-thread-6] Initializing /data/frans/MR_CHEST.hdr: [testng] 03:47:49,467 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:47:49,467 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:47:49,468 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-24_03-47-49.log] [testng] 03:47:49,468 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77ecc8f2 - End of configuration. [testng] [2024-11-24 03:47:49,893] [pool-1-thread-5] Initializing /data/frans/CT_KNEE.hdr: [testng] 03:47:49,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:47:49,893 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:47:49,894 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-24_03-47-49.log] [testng] 03:47:49,894 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36f0fc35 - End of configuration. [testng] [2024-11-24 03:47:50,324] [pool-1-thread-4] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1.img.hdr: [testng] 03:47:50,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:47:50,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:47:50,325 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-24_03-47-50.log] [testng] 03:47:50,325 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f8c191d - End of configuration. [testng] [2024-11-24 03:47:50,768] [pool-1-thread-3] Initializing /data/frans/CT_HAND.hdr: [testng] 03:47:50,768 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:47:50,769 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:47:50,769 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-24_03-47-50.log] [testng] 03:47:50,769 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e022fad - End of configuration. [testng] [2024-11-24 03:47:51,190] [pool-1-thread-2] Initializing /data/frans/Test Files for Frans/06-101-mask-40pc2dil.hdr: [testng] 03:47:51,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:47:51,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:47:51,191 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-24_03-47-51.log] [testng] 03:47:51,192 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6431fcbd - End of configuration. [testng] [2024-11-24 03:48:00,807] [pool-1-thread-2] Initializing /data/frans/MR_SEGBRAIN.hdr: [testng] [2024-11-24 03:48:01,317] [pool-1-thread-11] Initializing /data/frans/m000-MR_CHEST.gif: [testng] [2024-11-24 03:48:01,465] [pool-1-thread-3] Initializing /data/frans/CT_WHOLE.hdr: [testng] [2024-11-24 03:48:02,190] [pool-1-thread-6] Initializing /data/frans/brodmann.hdr: [testng] [2024-11-24 03:48:03,046] [pool-1-thread-5] Initializing /data/frans/CT_FOOT.hdr: [testng] [2024-11-24 03:48:03,759] [pool-1-thread-9] Initializing /data/frans/Test Files for Frans/F005_1002_MF_SCAN1_stat_brain_fdg_JJ_Volume_Corrected.hdr: [testng] [2024-11-24 03:48:04,403] [pool-1-thread-10] Initializing /data/frans/Test Files for Frans/1002-sag-transform-box-est_flip-ord.hdr: [testng] [2024-11-24 03:48:04,941] [pool-1-thread-7] Initializing /data/frans/Test Files for Frans/PLA-zm2-16mm_1002_MF_V1.hdr: [testng] [2024-11-24 03:48:05,395] [pool-1-thread-4] Initializing /data/frans/ch2.hdr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1113, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 58 seconds Finished: SUCCESS