Started by upstream project "BIOFORMATS-test-repo" build number 282 originally caused by: Started by user devspace 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/jenkins5605588173882698025.sh + '[' analyze = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_44550_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] 12:29:47,597 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 12:29:47,598 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 12:29:47,598 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:29:47,599 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 12:29:47,599 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 12:29:47,599 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 12:29:47,600 |-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] 12:29:47,600 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:29:47,600 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 12:29:47,600 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 12:29:47,600 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 12:29:47,601 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 12:29:47,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 12:29:47,814 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 12:29:47,840 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 12:29:47,840 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 12:29:47,848 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 12:29:47,848 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 12:29:47,848 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 12:29:47,848 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 12:29:47,848 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 12:29:47,849 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 12:29:47,849 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 249 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-06 12:29:47,858] [main] java.version = 1.8.0_342 [testng] 12:29:47,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 12:29:47,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:29:47,907 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-06_12-29-47.log] [testng] 12:29:47,909 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-06 12:29:47,910] [main] testng.directory = /data [testng] [2024-12-06 12:29:47,911] [main] testng.configDirectory = /config [testng] [2024-12-06 12:29:47,922] [main] testng.multiplier = 1.0 [testng] [2024-12-06 12:29:47,922] [main] testng.in-memory = false [testng] [2024-12-06 12:29:47,922] [main] testng.allow-missing = false [testng] [2024-12-06 12:29:47,922] [main] user.language = en [testng] [2024-12-06 12:29:47,922] [main] user.country = ${user.country} [testng] [2024-12-06 12:29:47,922] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-06 12:29:53,353] [main] ---------------------------------------- [testng] [2024-12-06 12:29:53,353] [main] Total files: 21 [testng] [2024-12-06 12:29:53,353] [main] Scan time: 5.43 s (258 ms/file) [testng] [2024-12-06 12:29:53,353] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-06 12:30:00,370] [pool-1-thread-1] Initializing /data/frans/m000-MR_CHEST.gif: [testng] 12:30:00,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 12:30:00,371 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:30:00,372 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-06_12-30-00.log] [testng] 12:30:00,372 |-INFO in ch.qos.logback.core.sift.SiftProcessor@640b9725 - End of configuration. [testng] [2024-12-06 12:30:00,484] [pool-1-thread-12] Initializing /data/frans/betmask.hdr: [testng] 12:30:00,485 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 12:30:00,485 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:30:00,485 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-06_12-30-00.log] [testng] 12:30:00,486 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63e81c6c - End of configuration. [testng] [2024-12-06 12:30:00,772] [pool-1-thread-11] Initializing /data/frans/Test Files for Frans/PLA-zm2-16mm_1002_MF_V1.hdr: [testng] 12:30:00,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 12:30:00,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:30:00,773 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-06_12-30-00.log] [testng] 12:30:00,773 |-INFO in ch.qos.logback.core.sift.SiftProcessor@425e85f3 - End of configuration. [testng] [2024-12-06 12:30:01,058] [pool-1-thread-10] Initializing /data/frans/MR_SEGBRAIN.hdr: [testng] 12:30:01,058 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 12:30:01,058 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:30:01,059 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-06_12-30-01.log] [testng] 12:30:01,059 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bee1669 - End of configuration. [testng] [2024-12-06 12:30:01,401] [pool-1-thread-9] Initializing /data/frans/Test Files for Frans/1002-sag-transform-box-est_flip-ord.hdr: [testng] 12:30:01,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 12:30:01,401 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:30:01,402 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-06_12-30-01.log] [testng] 12:30:01,402 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c48bf65 - End of configuration. [testng] [2024-12-06 12:30:01,686] [pool-1-thread-8] Initializing /data/frans/aal.hdr: [testng] 12:30:01,686 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 12:30:01,686 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:30:01,686 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-06_12-30-01.log] [testng] 12:30:01,687 |-INFO in ch.qos.logback.core.sift.SiftProcessor@171d401a - End of configuration. [testng] [2024-12-06 12:30:01,975] [pool-1-thread-7] Initializing /data/frans/CT_KNEE.hdr: [testng] 12:30:01,976 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 12:30:01,976 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:30:01,976 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-06_12-30-01.log] [testng] 12:30:01,977 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21185521 - End of configuration. [testng] [2024-12-06 12:30:02,274] [pool-1-thread-6] Initializing /data/frans/MR_CHEST.hdr: [testng] 12:30:02,274 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 12:30:02,274 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:30:02,275 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-06_12-30-02.log] [testng] 12:30:02,275 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4329f73 - End of configuration. [testng] [2024-12-06 12:30:02,563] [pool-1-thread-5] Initializing /data/frans/CT_CRANI.hdr: [testng] 12:30:02,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 12:30:02,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:30:02,564 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-06_12-30-02.log] [testng] 12:30:02,564 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ced025d - End of configuration. [testng] [2024-12-06 12:30:02,866] [pool-1-thread-4] Initializing /data/frans/ch2.hdr: [testng] 12:30:02,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 12:30:02,866 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:30:02,867 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-06_12-30-02.log] [testng] 12:30:02,867 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4775441e - End of configuration. [testng] [2024-12-06 12:30:03,148] [pool-1-thread-3] Initializing /data/frans/CT_WHOLE.hdr: [testng] 12:30:03,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 12:30:03,149 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:30:03,149 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-06_12-30-03.log] [testng] 12:30:03,150 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ce6dcd4 - End of configuration. [testng] [2024-12-06 12:30:03,461] [pool-1-thread-2] Initializing /data/frans/Test Files for Frans/F005_1002_MF_SCAN1_stat_brain_fdg_JJ_Volume_Corrected.hdr: [testng] 12:30:03,462 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 12:30:03,462 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 12:30:03,462 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-06_12-30-03.log] [testng] 12:30:03,463 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e51c0b3 - End of configuration. [testng] [2024-12-06 12:30:05,801] [pool-1-thread-1] Initializing /data/frans/CT_FOOT.hdr: [testng] [2024-12-06 12:30:08,174] [pool-1-thread-12] Initializing /data/frans/CT_CHEST.hdr: [testng] [2024-12-06 12:30:08,465] [pool-1-thread-11] Initializing /data/frans/brodmann.hdr: [testng] [2024-12-06 12:30:08,741] [pool-1-thread-2] Initializing /data/frans/Test Files for Frans/06-101-mask-40pc2dil.hdr: [testng] [2024-12-06 12:30:09,260] [pool-1-thread-8] Initializing /data/frans/Test Files for Frans/200-PLA_sansBD_spmT_0005.hdr: [testng] [2024-12-06 12:30:09,607] [pool-1-thread-4] Initializing /data/frans/ch2bet.hdr: [testng] [2024-12-06 12:30:09,974] [pool-1-thread-7] Initializing /data/frans/CT_HAND.hdr: [testng] [2024-12-06 12:30:10,299] [pool-1-thread-10] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1.img.hdr: [testng] [2024-12-06 12:30:10,618] [pool-1-thread-5] 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: 31 seconds Finished: SUCCESS