Started by upstream project "BIOFORMATS-test-repo" build number 129 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins17294282975314508020.sh + '[' analyze = slidebook ']' ++ date +%u + '[' 1 -le 1 ']' + DOCKER_ARGS='-Dtestng.memory=15g -Dtestng.threadCount=12 -Duser.language=fr -Duser.country=FR' + sudo docker run --rm --name BIOFORMATS-test-folder_20258_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 -Duser.language=fr -Duser.country=FR 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] 14:38:23,304 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 14:38:23,306 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 14:38:23,306 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 14:38:23,307 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 14:38:23,307 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 14:38:23,307 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 14:38:23,308 |-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] 14:38:23,308 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 14:38:23,308 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 14:38:23,308 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 14:38:23,309 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 14:38:23,309 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 14:38:23,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 14:38:23,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 14:38:23,592 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 14:38:23,593 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 14:38:23,602 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 14:38:23,602 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 14:38:23,602 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 14:38:23,603 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 14:38:23,603 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 14:38:23,604 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 14:38:23,604 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 296 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-22 14:38:23,615] [main] java.version = 1.8.0_342 [testng] 14:38:23,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 14:38:23,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:38:23,666 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-22_14-38-23.log] [testng] 14:38:23,668 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-07-22 14:38:23,670] [main] testng.directory = /data [testng] [2024-07-22 14:38:23,670] [main] testng.configDirectory = /config [testng] [2024-07-22 14:38:23,684] [main] testng.multiplier = 1.0 [testng] [2024-07-22 14:38:23,684] [main] testng.in-memory = false [testng] [2024-07-22 14:38:23,684] [main] testng.allow-missing = false [testng] [2024-07-22 14:38:23,684] [main] user.language = fr [testng] [2024-07-22 14:38:23,685] [main] user.country = FR [testng] [2024-07-22 14:38:23,685] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-07-22 14:38:24,417] [main] ---------------------------------------- [testng] [2024-07-22 14:38:24,417] [main] Total files: 21 [testng] [2024-07-22 14:38:24,417] [main] Scan time: 0.732 s (34 ms/file) [testng] [2024-07-22 14:38:24,417] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-22 14:38:25,687] [pool-1-thread-1] Initializing /data/frans/Test Files for Frans/PLA-zm2-16mm_1002_MF_V1.hdr: [testng] 14:38:25,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 14:38:25,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:38:25,688 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-22_14-38-25.log] [testng] 14:38:25,689 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5faa7d30 - End of configuration. [testng] [2024-07-22 14:38:25,744] [pool-1-thread-12] Initializing /data/frans/CT_HAND.hdr: [testng] 14:38:25,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 14:38:25,745 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:38:25,746 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-22_14-38-25.log] [testng] 14:38:25,746 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4756fbcc - End of configuration. [testng] [2024-07-22 14:38:25,762] [pool-1-thread-11] Initializing /data/frans/brodmann.hdr: [testng] 14:38:25,762 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 14:38:25,762 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:38:25,763 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-22_14-38-25.log] [testng] 14:38:25,764 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32f1b20 - End of configuration. [testng] [2024-07-22 14:38:25,779] [pool-1-thread-10] Initializing /data/frans/aal.hdr: [testng] 14:38:25,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 14:38:25,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:38:25,780 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-22_14-38-25.log] [testng] 14:38:25,780 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6897c46b - End of configuration. [testng] [2024-07-22 14:38:25,792] [pool-1-thread-9] Initializing /data/frans/Test Files for Frans/06-101-mask-40pc2dil.hdr: [testng] 14:38:25,792 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 14:38:25,792 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:38:25,793 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-22_14-38-25.log] [testng] 14:38:25,793 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e805a3 - End of configuration. [testng] [2024-07-22 14:38:25,813] [pool-1-thread-8] Initializing /data/frans/Test Files for Frans/200-PLA_sansBD_spmT_0005.hdr: [testng] 14:38:25,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 14:38:25,813 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:38:25,814 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-22_14-38-25.log] [testng] 14:38:25,815 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3ccee1f5 - End of configuration. [testng] [2024-07-22 14:38:25,830] [pool-1-thread-7] Initializing /data/frans/betmask.hdr: [testng] 14:38:25,830 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 14:38:25,830 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:38:25,831 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-22_14-38-25.log] [testng] 14:38:25,832 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26b09b2 - End of configuration. [testng] [2024-07-22 14:38:25,842] [pool-1-thread-6] Initializing /data/frans/CT_WHOLE.hdr: [testng] 14:38:25,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 14:38:25,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:38:25,843 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-22_14-38-25.log] [testng] 14:38:25,843 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7717f9e4 - End of configuration. [testng] [2024-07-22 14:38:25,853] [pool-1-thread-5] Initializing /data/frans/MR_SEGBRAIN.hdr: [testng] 14:38:25,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 14:38:25,853 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:38:25,854 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-22_14-38-25.log] [testng] 14:38:25,854 |-INFO in ch.qos.logback.core.sift.SiftProcessor@755508aa - End of configuration. [testng] [2024-07-22 14:38:25,864] [pool-1-thread-4] Initializing /data/frans/CT_FOOT.hdr: [testng] 14:38:25,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 14:38:25,864 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:38:25,865 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-22_14-38-25.log] [testng] 14:38:25,865 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5eefcd3d - End of configuration. [testng] [2024-07-22 14:38:25,876] [pool-1-thread-3] Initializing /data/frans/ch2bet.hdr: [testng] 14:38:25,876 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 14:38:25,876 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:38:25,877 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-22_14-38-25.log] [testng] 14:38:25,878 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13db8294 - End of configuration. [testng] [2024-07-22 14:38:25,904] [pool-1-thread-2] Initializing /data/frans/MR_CHEST.hdr: [testng] 14:38:25,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 14:38:25,905 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:38:25,905 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-22_14-38-25.log] [testng] 14:38:25,906 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a06bfa4 - End of configuration. [testng] [2024-07-22 14:38:27,553] [pool-1-thread-9] Initializing /data/frans/CT_CRANI.hdr: [testng] [2024-07-22 14:38:27,565] [pool-1-thread-3] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1.img.hdr: [testng] [2024-07-22 14:38:27,581] [pool-1-thread-11] Initializing /data/frans/CT_KNEE.hdr: [testng] [2024-07-22 14:38:27,591] [pool-1-thread-5] Initializing /data/frans/m000-MR_CHEST.gif: [testng] [2024-07-22 14:38:27,628] [pool-1-thread-10] Initializing /data/frans/CT_APERT.hdr: [testng] [2024-07-22 14:38:27,640] [pool-1-thread-6] Initializing /data/frans/CT_CHEST.hdr: [testng] [2024-07-22 14:38:27,655] [pool-1-thread-2] Initializing /data/frans/Test Files for Frans/F005_1002_MF_SCAN1_stat_brain_fdg_JJ_Volume_Corrected.hdr: [testng] [2024-07-22 14:38:27,665] [pool-1-thread-4] Initializing /data/frans/ch2.hdr: [testng] [2024-07-22 14:38:27,677] [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: 7 seconds Finished: SUCCESS