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Started by upstream project "BIOFORMATS-test-repo" build number 85 originally caused by: Started by upstream project "Trigger" build number 96 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins5490259769167497845.sh + '[' analyze = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_13042_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] 02:18:49,473 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:18:49,476 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 02:18:49,476 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:18:49,479 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:18:49,480 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:18:49,480 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:18:49,480 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:18:49,480 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:18:49,481 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:18:49,482 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:18:49,482 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:18:49,482 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:18:49,806 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:18:49,806 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:18:49,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:18:49,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:18:49,878 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:18:49,878 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:18:49,878 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:18:49,879 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:18:49,879 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 02:18:49,880 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 02:18:49,880 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 399 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-07 02:18:49,895] [main] java.version = 1.8.0_342 [testng] 02:18:49,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:18:49,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:49,962 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-07_02-18-49.log] [testng] 02:18:49,964 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-06-07 02:18:49,968] [main] testng.directory = /data [testng] [2024-06-07 02:18:49,968] [main] testng.configDirectory = /config [testng] [2024-06-07 02:18:49,989] [main] testng.multiplier = 1.0 [testng] [2024-06-07 02:18:49,990] [main] testng.in-memory = false [testng] [2024-06-07 02:18:49,990] [main] testng.allow-missing = false [testng] [2024-06-07 02:18:49,990] [main] user.language = en [testng] [2024-06-07 02:18:49,990] [main] user.country = ${user.country} [testng] [2024-06-07 02:18:49,990] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-06-07 02:18:50,799] [main] ---------------------------------------- [testng] [2024-06-07 02:18:50,799] [main] Total files: 21 [testng] [2024-06-07 02:18:50,799] [main] Scan time: 0.809 s (38 ms/file) [testng] [2024-06-07 02:18:50,799] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-07 02:18:52,359] [pool-1-thread-1] Initializing /data/frans/Test Files for Frans/PLA-zm2-16mm_1002_MF_V1.hdr: [testng] 02:18:52,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:18:52,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:52,361 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-07_02-18-52.log] [testng] 02:18:52,362 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a235c13 - End of configuration. [testng] [2024-06-07 02:18:52,430] [pool-1-thread-12] Initializing /data/frans/CT_HAND.hdr: [testng] 02:18:52,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:18:52,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:52,432 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-07_02-18-52.log] [testng] 02:18:52,432 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c3407ff - End of configuration. [testng] [2024-06-07 02:18:52,453] [pool-1-thread-11] Initializing /data/frans/brodmann.hdr: [testng] 02:18:52,454 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:18:52,454 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:52,455 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-07_02-18-52.log] [testng] 02:18:52,455 |-INFO in ch.qos.logback.core.sift.SiftProcessor@178b8206 - End of configuration. [testng] [2024-06-07 02:18:52,473] [pool-1-thread-10] Initializing /data/frans/aal.hdr: [testng] 02:18:52,473 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:18:52,474 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:52,475 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-07_02-18-52.log] [testng] 02:18:52,475 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26563289 - End of configuration. [testng] [2024-06-07 02:18:52,495] [pool-1-thread-9] Initializing /data/frans/Test Files for Frans/06-101-mask-40pc2dil.hdr: [testng] 02:18:52,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:18:52,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:52,496 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-07_02-18-52.log] [testng] 02:18:52,497 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b19f54c - End of configuration. [testng] [2024-06-07 02:18:52,513] [pool-1-thread-8] Initializing /data/frans/Test Files for Frans/200-PLA_sansBD_spmT_0005.hdr: [testng] 02:18:52,513 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:18:52,514 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:52,514 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-07_02-18-52.log] [testng] 02:18:52,515 |-INFO in ch.qos.logback.core.sift.SiftProcessor@725dd4c3 - End of configuration. [testng] [2024-06-07 02:18:52,530] [pool-1-thread-7] Initializing /data/frans/betmask.hdr: [testng] 02:18:52,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:18:52,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:52,531 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-07_02-18-52.log] [testng] 02:18:52,532 |-INFO in ch.qos.logback.core.sift.SiftProcessor@755508aa - End of configuration. [testng] [2024-06-07 02:18:52,545] [pool-1-thread-6] Initializing /data/frans/CT_WHOLE.hdr: [testng] 02:18:52,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:18:52,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:52,546 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-07_02-18-52.log] [testng] 02:18:52,546 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5eefcd3d - End of configuration. [testng] [2024-06-07 02:18:52,560] [pool-1-thread-5] Initializing /data/frans/MR_SEGBRAIN.hdr: [testng] 02:18:52,560 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:18:52,560 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:52,561 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-07_02-18-52.log] [testng] 02:18:52,561 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13db8294 - End of configuration. [testng] [2024-06-07 02:18:52,576] [pool-1-thread-4] Initializing /data/frans/CT_FOOT.hdr: [testng] 02:18:52,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:18:52,576 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:52,577 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-07_02-18-52.log] [testng] 02:18:52,577 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a06bfa4 - End of configuration. [testng] [2024-06-07 02:18:52,593] [pool-1-thread-3] Initializing /data/frans/ch2bet.hdr: [testng] 02:18:52,593 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:18:52,593 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:52,594 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-07_02-18-52.log] [testng] 02:18:52,594 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60a8d175 - End of configuration. [testng] [2024-06-07 02:18:52,619] [pool-1-thread-2] Initializing /data/frans/MR_CHEST.hdr: [testng] 02:18:52,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:18:52,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:18:52,620 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-07_02-18-52.log] [testng] 02:18:52,620 |-INFO in ch.qos.logback.core.sift.SiftProcessor@568c8ef5 - End of configuration. [testng] [2024-06-07 02:18:54,999] [pool-1-thread-9] Initializing /data/frans/CT_CRANI.hdr: [testng] [2024-06-07 02:18:55,013] [pool-1-thread-2] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1.img.hdr: [testng] [2024-06-07 02:18:55,026] [pool-1-thread-11] Initializing /data/frans/CT_KNEE.hdr: [testng] [2024-06-07 02:18:55,038] [pool-1-thread-10] Initializing /data/frans/m000-MR_CHEST.gif: [testng] [2024-06-07 02:18:55,067] [pool-1-thread-5] Initializing /data/frans/CT_APERT.hdr: [testng] [2024-06-07 02:18:55,087] [pool-1-thread-6] Initializing /data/frans/CT_CHEST.hdr: [testng] [2024-06-07 02:18:55,101] [pool-1-thread-3] Initializing /data/frans/Test Files for Frans/F005_1002_MF_SCAN1_stat_brain_fdg_JJ_Volume_Corrected.hdr: [testng] [2024-06-07 02:18:55,114] [pool-1-thread-4] Initializing /data/frans/ch2.hdr: [testng] [2024-06-07 02:18:55,129] [pool-1-thread-12] Initializing /data/frans/Test Files for Frans/1002-sag-transform-box-est_flip-ord.hdr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1113, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 10 seconds Finished: SUCCESS