Started by upstream project "BIOFORMATS-test-repo" build number 222 originally caused by: Started by upstream project "Trigger" build number 249 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins2142862667106129603.sh + '[' leica-tcs = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35331_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] 21:06:40,370 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 21:06:40,371 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 21:06:40,371 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 21:06:40,372 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 21:06:40,373 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 21:06:40,373 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 21:06:40,373 |-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] 21:06:40,373 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 21:06:40,374 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 21:06:40,374 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 21:06:40,375 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 21:06:40,375 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 21:06:40,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 21:06:40,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 21:06:40,557 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 21:06:40,557 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 21:06:40,562 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 21:06:40,562 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 21:06:40,562 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 21:06:40,562 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 21:06:40,562 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 21:06:40,564 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 21:06:40,564 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 190 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-16 21:06:40,572] [main] java.version = 17.0.2 [testng] 21:06:40,575 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 21:06:40,575 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 21:06:40,615 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-16_21-06-40.log] [testng] 21:06:40,616 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-10-16 21:06:40,618] [main] testng.directory = /data [testng] [2024-10-16 21:06:40,618] [main] testng.configDirectory = /config [testng] [2024-10-16 21:06:40,626] [main] testng.multiplier = 1.0 [testng] [2024-10-16 21:06:40,627] [main] testng.in-memory = false [testng] [2024-10-16 21:06:40,627] [main] testng.allow-missing = false [testng] [2024-10-16 21:06:40,627] [main] user.language = en [testng] [2024-10-16 21:06:40,627] [main] user.country = ${user.country} [testng] [2024-10-16 21:06:40,627] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-16 21:07:16,738] [main] ---------------------------------------- [testng] [2024-10-16 21:07:16,739] [main] Total files: 944 [testng] [2024-10-16 21:07:16,739] [main] Scan time: 36.11 s (38 ms/file) [testng] [2024-10-16 21:07:16,739] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-16 21:14:00,703] [pool-1-thread-1] Initializing /data/stjude/AntoDayzerocy3GRP.tif: [testng] 21:14:00,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 21:14:00,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 21:14:00,704 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-16_21-14-00.log] [testng] 21:14:00,704 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1383804 - End of configuration. [testng] [2024-10-16 21:14:09,097] [pool-1-thread-12] Initializing /data/brian/Series002_z00_ch00.tif: [testng] 21:14:09,097 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 21:14:09,097 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 21:14:09,097 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-16_21-14-09.log] [testng] 21:14:09,098 |-INFO in ch.qos.logback.core.sift.SiftProcessor@648de2ba - End of configuration. [testng] [2024-10-16 21:14:16,309] [pool-1-thread-11] Initializing /data/martin/Series028_z00_ch00.tif: [testng] 21:14:16,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 21:14:16,309 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 21:14:16,309 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-16_21-14-16.log] [testng] 21:14:16,310 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36338337 - End of configuration. [testng] [2024-10-16 21:14:26,944] [pool-1-thread-10] Initializing /data/stjude/AntoDay4dblmy2GRP.tif: [testng] 21:14:26,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 21:14:26,944 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 21:14:26,945 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-16_21-14-26.log] [testng] 21:14:26,945 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d6a01f - End of configuration. [testng] [2024-10-16 21:14:36,066] [pool-1-thread-9] Initializing /data/brian/Series002_z01.tif: [testng] 21:14:36,066 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 21:14:36,066 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 21:14:36,067 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-16_21-14-36.log] [testng] 21:14:36,067 |-INFO in ch.qos.logback.core.sift.SiftProcessor@783cb46 - End of configuration. [testng] [2024-10-16 21:14:46,180] [pool-1-thread-8] Initializing /data/primate/Leica_Image.tif: [testng] 21:14:46,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 21:14:46,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 21:14:46,181 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-16_21-14-46.log] [testng] 21:14:46,182 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5aa0721d - End of configuration. [testng] [2024-10-16 21:14:52,244] [pool-1-thread-7] Initializing /data/stjude/AntoDayzerocy3OVP.tif: [testng] 21:14:52,244 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 21:14:52,244 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 21:14:52,245 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-16_21-14-52.log] [testng] 21:14:52,245 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e8a4f - End of configuration. [testng] [2024-10-16 21:15:00,721] [pool-1-thread-6] Initializing /data/stjude/Antoday1dblmysglGRP.tif: [testng] 21:15:00,721 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 21:15:00,721 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 21:15:00,722 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-16_21-15-00.log] [testng] 21:15:00,722 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f50f29e - End of configuration. [testng] [2024-10-16 21:15:09,175] [pool-1-thread-5] Initializing /data/stjude/Antoday1dblcatsglGRP.tif: [testng] 21:15:09,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 21:15:09,175 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 21:15:09,176 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-16_21-15-09.log] [testng] 21:15:09,176 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4697ea3b - End of configuration. [testng] [2024-10-16 21:15:15,237] [pool-1-thread-4] Initializing /data/stjude/AntoDay4dblmyGRP.tif: [testng] 21:15:15,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 21:15:15,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 21:15:15,238 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-16_21-15-15.log] [testng] 21:15:15,239 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b196d81 - End of configuration. [testng] [2024-10-16 21:15:22,544] [pool-1-thread-3] Initializing /data/stjude/AntoDay1dblGRP.tif: [testng] 21:15:22,544 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 21:15:22,544 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 21:15:22,545 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-16_21-15-22.log] [testng] 21:15:22,545 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1fd8fba9 - End of configuration. [testng] [2024-10-16 21:15:30,515] [pool-1-thread-2] Initializing /data/stjude/AntoDay1cy3/c01f0001.TIF: [testng] 21:15:30,515 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 21:15:30,516 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 21:15:30,516 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-16_21-15-30.log] [testng] 21:15:30,516 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a56bb7b - End of configuration. [testng] [2024-10-16 21:16:14,949] [pool-1-thread-2] Initializing /data/stjude/AntoDay4dblcatdataGRP.tif: [testng] [2024-10-16 21:16:21,270] [pool-1-thread-8] Initializing /data/stjude/Antoday1dblcat2dataGRP.tif: [testng] [2024-10-16 21:16:36,905] [pool-1-thread-9] Initializing /data/dave/series 35/042911_Series035_t00_z000_ch00.tif: Build was aborted Calling Pipeline was cancelled Finished: ABORTED