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Started by upstream project "BIOFORMATS-test-repo" build number 117 originally caused by: Started by upstream project "Trigger" build number 134 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/jenkins12935448902510675299.sh + '[' analyze = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_18290_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings 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] 02:16:48,551 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:16:48,552 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 02:16:48,552 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:16:48,553 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:16:48,553 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:16:48,553 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:16:48,554 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:16:48,554 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:16:48,554 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:16:48,555 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:16:48,555 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:16:48,555 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:16:48,736 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:16:48,736 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:16:48,762 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:16:48,762 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:16:48,769 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:16:48,769 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:16:48,770 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:16:48,770 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:16:48,770 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 02:16:48,771 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 02:16:48,771 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 217 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-07-11 02:16:48,781] [main] java.version = 21 [testng] 02:16:48,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:16:48,785 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:48,828 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-11_02-16-48.log] [testng] 02:16:48,829 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-07-11 02:16:48,831] [main] testng.directory = /data [testng] [2024-07-11 02:16:48,831] [main] testng.configDirectory = /config [testng] [2024-07-11 02:16:48,840] [main] testng.multiplier = 1.0 [testng] [2024-07-11 02:16:48,841] [main] testng.in-memory = false [testng] [2024-07-11 02:16:48,841] [main] testng.allow-missing = false [testng] [2024-07-11 02:16:48,841] [main] user.language = en [testng] [2024-07-11 02:16:48,841] [main] user.country = ${user.country} [testng] [2024-07-11 02:16:48,841] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-07-11 02:16:49,438] [main] ---------------------------------------- [testng] [2024-07-11 02:16:49,438] [main] Total files: 21 [testng] [2024-07-11 02:16:49,438] [main] Scan time: 0.597 s (28 ms/file) [testng] [2024-07-11 02:16:49,438] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-07-11 02:16:50,656] [pool-1-thread-1] Initializing /data/frans/Test Files for Frans/PLA-zm2-16mm_1002_MF_V1.hdr: [testng] 02:16:50,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:16:50,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:50,657 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-11_02-16-50.log] [testng] 02:16:50,658 |-INFO in ch.qos.logback.core.sift.SiftProcessor@42ed655c - End of configuration. [testng] [2024-07-11 02:16:50,684] [pool-1-thread-12] Initializing /data/frans/brodmann.hdr: [testng] 02:16:50,684 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:16:50,684 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:50,686 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-11_02-16-50.log] [testng] 02:16:50,687 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26c20cae - End of configuration. [testng] [2024-07-11 02:16:50,714] [pool-1-thread-11] Initializing /data/frans/Test Files for Frans/06-101-mask-40pc2dil.hdr: [testng] 02:16:50,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:16:50,715 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:50,715 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-11_02-16-50.log] [testng] 02:16:50,716 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ec3d075 - End of configuration. [testng] [2024-07-11 02:16:50,729] [pool-1-thread-10] Initializing /data/frans/CT_KNEE.hdr: [testng] 02:16:50,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:16:50,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:50,731 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-11_02-16-50.log] [testng] 02:16:50,731 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c45e76a - End of configuration. [testng] [2024-07-11 02:16:50,748] [pool-1-thread-9] Initializing /data/frans/MR_SEGBRAIN.hdr: [testng] 02:16:50,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:16:50,748 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:50,749 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-11_02-16-50.log] [testng] 02:16:50,749 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13222ddf - End of configuration. [testng] [2024-07-11 02:16:50,761] [pool-1-thread-8] Initializing /data/frans/betmask.hdr: [testng] 02:16:50,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:16:50,761 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:50,762 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-11_02-16-50.log] [testng] 02:16:50,763 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f2c3c45 - End of configuration. [testng] [2024-07-11 02:16:50,776] [pool-1-thread-7] Initializing /data/frans/ch2.hdr: [testng] 02:16:50,777 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:16:50,777 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:50,778 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-11_02-16-50.log] [testng] 02:16:50,778 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79bd8b34 - End of configuration. [testng] [2024-07-11 02:16:50,790] [pool-1-thread-6] Initializing /data/frans/CT_HAND.hdr: [testng] 02:16:50,790 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:16:50,791 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:50,791 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-11_02-16-50.log] [testng] 02:16:50,792 |-INFO in ch.qos.logback.core.sift.SiftProcessor@699338c9 - End of configuration. [testng] [2024-07-11 02:16:50,804] [pool-1-thread-5] Initializing /data/frans/CT_CRANI.hdr: [testng] 02:16:50,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:16:50,804 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:50,805 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-11_02-16-50.log] [testng] 02:16:50,805 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c91393b - End of configuration. [testng] [2024-07-11 02:16:50,817] [pool-1-thread-4] Initializing /data/frans/ch2bet.hdr: [testng] 02:16:50,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:16:50,817 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:50,818 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-11_02-16-50.log] [testng] 02:16:50,818 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7cc25ff0 - End of configuration. [testng] [2024-07-11 02:16:50,829] [pool-1-thread-3] Initializing /data/frans/CT_FOOT.hdr: [testng] 02:16:50,830 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:16:50,830 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:50,830 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-11_02-16-50.log] [testng] 02:16:50,831 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a1dddc9 - End of configuration. [testng] [2024-07-11 02:16:50,842] [pool-1-thread-2] Initializing /data/frans/MR_CHEST.hdr: [testng] 02:16:50,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:16:50,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:16:50,843 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-11_02-16-50.log] [testng] 02:16:50,844 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4283052f - End of configuration. [testng] [2024-07-11 02:16:52,430] [pool-1-thread-1] Initializing /data/frans/m000-MR_CHEST.gif: [testng] [2024-07-11 02:16:52,449] [pool-1-thread-8] Initializing /data/frans/aal.hdr: [testng] [2024-07-11 02:16:52,460] [pool-1-thread-11] Initializing /data/frans/CT_WHOLE.hdr: [testng] [2024-07-11 02:16:52,908] [pool-1-thread-9] Initializing /data/frans/Test Files for Frans/1002-sag-transform-box-est_flip-ord.hdr: [testng] [2024-07-11 02:16:52,921] [pool-1-thread-4] Initializing /data/frans/Test Files for Frans/F005_1002_MF_SCAN1_stat_brain_fdg_JJ_Volume_Corrected.hdr: [testng] [2024-07-11 02:16:52,933] [pool-1-thread-10] Initializing /data/frans/Test Files for Frans/200-PLA_sansBD_spmT_0005.hdr: [testng] [2024-07-11 02:16:52,944] [pool-1-thread-6] Initializing /data/frans/CT_CHEST.hdr: [testng] [2024-07-11 02:16:52,955] [pool-1-thread-7] Initializing /data/frans/CT_APERT.hdr: [testng] [2024-07-11 02:16:52,963] [pool-1-thread-3] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1.img.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