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Started by upstream project "BIOFORMATS-test-repo" build number 229 originally caused by: Started by upstream project "Trigger" build number 254 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins9805297601251605516.sh + '[' analyze = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35984_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] 03:38:38,677 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:38:38,678 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 03:38:38,678 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:38:38,679 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:38:38,679 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:38:38,680 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:38:38,680 |-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] 03:38:38,680 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:38:38,680 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:38:38,681 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:38:38,681 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:38:38,681 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:38:38,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:38:38,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:38:38,861 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:38:38,861 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:38:38,867 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:38:38,867 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:38:38,867 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:38:38,868 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:38:38,868 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 03:38:38,868 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 03:38:38,868 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 188 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-20 03:38:38,877] [main] java.version = 17.0.2 [testng] 03:38:38,881 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:38:38,881 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:38:38,941 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-20_03-38-38.log] [testng] 03:38:38,943 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-10-20 03:38:38,946] [main] testng.directory = /data [testng] [2024-10-20 03:38:38,947] [main] testng.configDirectory = /config [testng] [2024-10-20 03:38:38,958] [main] testng.multiplier = 1.0 [testng] [2024-10-20 03:38:38,959] [main] testng.in-memory = false [testng] [2024-10-20 03:38:38,959] [main] testng.allow-missing = false [testng] [2024-10-20 03:38:38,959] [main] user.language = en [testng] [2024-10-20 03:38:38,959] [main] user.country = ${user.country} [testng] [2024-10-20 03:38:38,960] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-20 03:38:43,896] [main] ---------------------------------------- [testng] [2024-10-20 03:38:43,896] [main] Total files: 21 [testng] [2024-10-20 03:38:43,896] [main] Scan time: 4.936 s (235 ms/file) [testng] [2024-10-20 03:38:43,896] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 21 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-20 03:38:49,848] [pool-1-thread-1] Initializing /data/frans/CT_CRANI.hdr: [testng] 03:38:49,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:38:49,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:38:49,850 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-20_03-38-49.log] [testng] 03:38:49,851 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45656201 - End of configuration. [testng] [2024-10-20 03:38:50,305] [pool-1-thread-12] Initializing /data/frans/aal.hdr: [testng] 03:38:50,306 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:38:50,306 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:38:50,307 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-20_03-38-50.log] [testng] 03:38:50,307 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e4d762f - End of configuration. [testng] [2024-10-20 03:38:50,687] [pool-1-thread-11] Initializing /data/frans/CT_APERT.hdr: [testng] 03:38:50,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:38:50,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:38:50,688 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-20_03-38-50.log] [testng] 03:38:50,688 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59bfa464 - End of configuration. [testng] [2024-10-20 03:38:50,855] [pool-1-thread-10] Initializing /data/frans/Test Files for Frans/200-PLA_sansBD_spmT_0005.hdr: [testng] 03:38:50,855 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:38:50,855 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:38:50,856 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-20_03-38-50.log] [testng] 03:38:50,856 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7beb973d - End of configuration. [testng] [2024-10-20 03:38:51,044] [pool-1-thread-9] Initializing /data/frans/CT_CHEST.hdr: [testng] 03:38:51,044 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:38:51,044 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:38:51,045 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-20_03-38-51.log] [testng] 03:38:51,046 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a64d02e - End of configuration. [testng] [2024-10-20 03:38:51,254] [pool-1-thread-8] Initializing /data/frans/ch2bet.hdr: [testng] 03:38:51,254 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:38:51,254 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:38:51,255 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-20_03-38-51.log] [testng] 03:38:51,255 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2638dc46 - End of configuration. [testng] [2024-10-20 03:38:51,430] [pool-1-thread-7] Initializing /data/frans/betmask.hdr: [testng] 03:38:51,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:38:51,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:38:51,431 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-20_03-38-51.log] [testng] 03:38:51,432 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d0fff1 - End of configuration. [testng] [2024-10-20 03:38:51,607] [pool-1-thread-6] Initializing /data/frans/MR_CHEST.hdr: [testng] 03:38:51,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:38:51,608 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:38:51,609 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-20_03-38-51.log] [testng] 03:38:51,609 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ef384dd - End of configuration. [testng] [2024-10-20 03:38:51,794] [pool-1-thread-5] Initializing /data/frans/CT_KNEE.hdr: [testng] 03:38:51,795 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:38:51,795 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:38:51,795 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-20_03-38-51.log] [testng] 03:38:51,796 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ff965f2 - End of configuration. [testng] [2024-10-20 03:38:51,999] [pool-1-thread-4] Initializing /data/frans/eNlf-02-05-08-rats25-28_v1.img.hdr: [testng] 03:38:51,999 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:38:51,999 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:38:52,000 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-20_03-38-51.log] [testng] 03:38:52,000 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11e0d101 - End of configuration. [testng] [2024-10-20 03:38:52,194] [pool-1-thread-3] Initializing /data/frans/CT_HAND.hdr: [testng] 03:38:52,194 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:38:52,195 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:38:52,195 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-20_03-38-52.log] [testng] 03:38:52,196 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a54b9bf - End of configuration. [testng] [2024-10-20 03:38:52,384] [pool-1-thread-2] Initializing /data/frans/Test Files for Frans/06-101-mask-40pc2dil.hdr: [testng] 03:38:52,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:38:52,384 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:38:52,384 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-20_03-38-52.log] [testng] 03:38:52,385 |-INFO in ch.qos.logback.core.sift.SiftProcessor@bf8a947 - End of configuration. [testng] [2024-10-20 03:38:58,554] [pool-1-thread-7] Initializing /data/frans/MR_SEGBRAIN.hdr: [testng] [2024-10-20 03:38:58,761] [pool-1-thread-11] Initializing /data/frans/m000-MR_CHEST.gif: [testng] [2024-10-20 03:38:58,829] [pool-1-thread-12] Initializing /data/frans/CT_WHOLE.hdr: [testng] [2024-10-20 03:38:59,010] [pool-1-thread-8] Initializing /data/frans/brodmann.hdr: [testng] [2024-10-20 03:38:59,235] [pool-1-thread-1] Initializing /data/frans/CT_FOOT.hdr: [testng] [2024-10-20 03:38:59,384] [pool-1-thread-6] Initializing /data/frans/Test Files for Frans/F005_1002_MF_SCAN1_stat_brain_fdg_JJ_Volume_Corrected.hdr: [testng] [2024-10-20 03:38:59,626] [pool-1-thread-5] Initializing /data/frans/Test Files for Frans/1002-sag-transform-box-est_flip-ord.hdr: [testng] [2024-10-20 03:39:00,042] [pool-1-thread-9] Initializing /data/frans/Test Files for Frans/PLA-zm2-16mm_1002_MF_V1.hdr: [testng] [2024-10-20 03:39:00,500] [pool-1-thread-3] 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: 30 seconds Finished: SUCCESS