Started by upstream project "BIOFORMATS-test-repo" build number 236 originally caused by: Started by upstream project "Trigger" build number 261 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/jenkins6253889432189770358.sh + '[' leica-tcs = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_37163_merge_ci -v /uod/idr/repos/curated/leica-tcs:/data -v /uod/idr-scratch/merge-ci/curated/leica-tcs:/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] 03:36:57,445 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:36:57,446 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 03:36:57,446 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:36:57,447 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:36:57,448 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:36:57,448 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:36:57,449 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 03:36:57,449 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:36:57,449 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:36:57,450 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:36:57,450 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:36:57,450 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:36:57,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:36:57,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:36:57,642 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:36:57,642 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:36:57,648 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:36:57,648 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:36:57,648 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:36:57,648 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:36:57,648 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 03:36:57,649 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 03:36:57,649 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 200 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-27 03:36:57,658] [main] java.version = 17.0.2 [testng] 03:36:57,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:36:57,662 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:36:57,703 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-27_03-36-57.log] [testng] 03:36:57,704 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-10-27 03:36:57,707] [main] testng.directory = /data [testng] [2024-10-27 03:36:57,707] [main] testng.configDirectory = /config [testng] [2024-10-27 03:36:57,716] [main] testng.multiplier = 1.0 [testng] [2024-10-27 03:36:57,717] [main] testng.in-memory = false [testng] [2024-10-27 03:36:57,717] [main] testng.allow-missing = false [testng] [2024-10-27 03:36:57,717] [main] user.language = en [testng] [2024-10-27 03:36:57,717] [main] user.country = ${user.country} [testng] [2024-10-27 03:36:57,717] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-27 03:37:27,440] [main] ---------------------------------------- [testng] [2024-10-27 03:37:27,441] [main] Total files: 944 [testng] [2024-10-27 03:37:27,441] [main] Scan time: 29.723 s (31 ms/file) [testng] [2024-10-27 03:37:27,441] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-27 03:39:04,280] [pool-1-thread-1] Initializing /data/stjude/AntoDayzerocy3GRP.tif: [testng] 03:39:04,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:39:04,280 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:39:04,282 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-27_03-39-04.log] [testng] 03:39:04,282 |-INFO in ch.qos.logback.core.sift.SiftProcessor@445bf84d - End of configuration. [testng] [2024-10-27 03:39:05,917] [pool-1-thread-12] Initializing /data/brian/Series002_z00_ch00.tif: [testng] 03:39:05,917 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:39:05,917 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:39:05,918 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-27_03-39-05.log] [testng] 03:39:05,918 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f5eb0ce - End of configuration. [testng] [2024-10-27 03:39:07,196] [pool-1-thread-11] Initializing /data/martin/Series028_z00_ch00.tif: [testng] 03:39:07,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:39:07,197 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:39:07,197 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-27_03-39-07.log] [testng] 03:39:07,198 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4137d3bd - End of configuration. [testng] [2024-10-27 03:39:08,975] [pool-1-thread-10] Initializing /data/stjude/AntoDay4dblmy2GRP.tif: [testng] 03:39:08,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:39:08,975 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:39:08,976 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-27_03-39-08.log] [testng] 03:39:08,976 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a2395dc - End of configuration. [testng] [2024-10-27 03:39:10,403] [pool-1-thread-9] Initializing /data/brian/Series002_z01.tif: [testng] 03:39:10,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:39:10,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:39:10,404 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-27_03-39-10.log] [testng] 03:39:10,404 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b923de7 - End of configuration. [testng] [2024-10-27 03:39:12,417] [pool-1-thread-8] Initializing /data/primate/Leica_Image.tif: [testng] 03:39:12,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:39:12,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:39:12,418 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-27_03-39-12.log] [testng] 03:39:12,418 |-INFO in ch.qos.logback.core.sift.SiftProcessor@294c9bdc - End of configuration. [testng] [2024-10-27 03:39:13,705] [pool-1-thread-7] Initializing /data/stjude/AntoDayzerocy3OVP.tif: [testng] 03:39:13,705 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:39:13,705 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:39:13,706 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-27_03-39-13.log] [testng] 03:39:13,706 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f40e557 - End of configuration. [testng] [2024-10-27 03:39:15,154] [pool-1-thread-6] Initializing /data/stjude/Antoday1dblmysglGRP.tif: [testng] 03:39:15,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:39:15,154 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:39:15,155 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-27_03-39-15.log] [testng] 03:39:15,155 |-INFO in ch.qos.logback.core.sift.SiftProcessor@675ff2bf - End of configuration. [testng] [2024-10-27 03:39:16,471] [pool-1-thread-5] Initializing /data/stjude/Antoday1dblcatsglGRP.tif: [testng] 03:39:16,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:39:16,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:39:16,472 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-27_03-39-16.log] [testng] 03:39:16,473 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ac7fc2e - End of configuration. [testng] [2024-10-27 03:39:17,808] [pool-1-thread-4] Initializing /data/stjude/AntoDay4dblmyGRP.tif: [testng] 03:39:17,808 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:39:17,808 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:39:17,809 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-27_03-39-17.log] [testng] 03:39:17,810 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5aa0721d - End of configuration. [testng] [2024-10-27 03:39:19,140] [pool-1-thread-3] Initializing /data/stjude/AntoDay1dblGRP.tif: [testng] 03:39:19,141 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:39:19,141 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:39:19,141 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-27_03-39-19.log] [testng] 03:39:19,142 |-INFO in ch.qos.logback.core.sift.SiftProcessor@121c8b03 - End of configuration. [testng] [2024-10-27 03:39:20,564] [pool-1-thread-2] Initializing /data/stjude/AntoDay1cy3/c01f0001.TIF: [testng] 03:39:20,565 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:39:20,565 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:39:20,565 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-27_03-39-20.log] [testng] 03:39:20,566 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e8a4f - End of configuration. [testng] [2024-10-27 03:39:30,157] [pool-1-thread-2] Initializing /data/stjude/AntoDay4dblcatdataGRP.tif: [testng] [2024-10-27 03:39:31,846] [pool-1-thread-8] Initializing /data/stjude/Antoday1dblcat2dataGRP.tif: [testng] [2024-10-27 03:39:34,678] [pool-1-thread-9] Initializing /data/dave/series 35/042911_Series035_t00_z000_ch00.tif: [testng] 04:45:51,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:45:51,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:45:51,219 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-27_04-45-51.log] [testng] 04:45:51,219 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78422efb - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 795, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 68 minutes 58 seconds Finished: SUCCESS