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Started by upstream project "BIOFORMATS-test-repo" build number 287 originally caused by: Started by upstream project "Trigger" build number 306 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@10 [BIOFORMATS-test-folder@10] $ /bin/bash -xe /tmp/jenkins14760912323597378246.sh + '[' leica-tcs = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_45400_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] 05:44:23,109 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 05:44:23,111 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 05:44:23,111 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:44:23,112 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:44:23,112 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 05:44:23,112 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 05:44:23,113 |-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] 05:44:23,113 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:44:23,113 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:44:23,114 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 05:44:23,114 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 05:44:23,114 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 05:44:23,302 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 05:44:23,302 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 05:44:23,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 05:44:23,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 05:44:23,329 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 05:44:23,329 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 05:44:23,329 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 05:44:23,330 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 05:44:23,330 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 05:44:23,331 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 05:44:23,331 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 218 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-11 05:44:23,340] [main] java.version = 17.0.2 [testng] 05:44:23,343 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:44:23,343 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:44:23,384 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-11_05-44-23.log] [testng] 05:44:23,385 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-12-11 05:44:23,387] [main] testng.directory = /data [testng] [2024-12-11 05:44:23,387] [main] testng.configDirectory = /config [testng] [2024-12-11 05:44:23,396] [main] testng.multiplier = 1.0 [testng] [2024-12-11 05:44:23,396] [main] testng.in-memory = false [testng] [2024-12-11 05:44:23,396] [main] testng.allow-missing = false [testng] [2024-12-11 05:44:23,396] [main] user.language = en [testng] [2024-12-11 05:44:23,397] [main] user.country = ${user.country} [testng] [2024-12-11 05:44:23,397] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-11 05:44:42,603] [main] ---------------------------------------- [testng] [2024-12-11 05:44:42,604] [main] Total files: 944 [testng] [2024-12-11 05:44:42,604] [main] Scan time: 19.206 s (20 ms/file) [testng] [2024-12-11 05:44:42,604] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-11 05:46:56,232] [pool-1-thread-1] Initializing /data/stjude/Antoday1dblcat2dataGRP.tif: [testng] 05:46:56,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 05:46:56,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:46:56,234 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-11_05-46-56.log] [testng] 05:46:56,234 |-INFO in ch.qos.logback.core.sift.SiftProcessor@369d8c4e - End of configuration. [testng] [2024-12-11 05:46:58,029] [pool-1-thread-12] Initializing /data/stjude/AntoDay4dblcatdataGRP.tif: [testng] 05:46:58,029 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 05:46:58,029 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:46:58,029 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-11_05-46-58.log] [testng] 05:46:58,030 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67bee2ae - End of configuration. [testng] [2024-12-11 05:47:00,007] [pool-1-thread-11] Initializing /data/stjude/Antoday1dblmysglGRP.tif: [testng] 05:47:00,007 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 05:47:00,007 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:47:00,008 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-11_05-47-00.log] [testng] 05:47:00,008 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64482366 - End of configuration. [testng] [2024-12-11 05:47:01,738] [pool-1-thread-10] Initializing /data/brian/Series002_z01.tif: [testng] 05:47:01,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 05:47:01,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:47:01,739 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-11_05-47-01.log] [testng] 05:47:01,739 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37bd9e96 - End of configuration. [testng] [2024-12-11 05:47:04,374] [pool-1-thread-9] Initializing /data/stjude/AntoDay1dblGRP.tif: [testng] 05:47:04,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 05:47:04,374 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:47:04,374 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-11_05-47-04.log] [testng] 05:47:04,375 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f5d248 - End of configuration. [testng] [2024-12-11 05:47:06,890] [pool-1-thread-8] Initializing /data/martin/Series028_z00_ch00.tif: [testng] 05:47:06,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 05:47:06,890 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:47:06,891 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-11_05-47-06.log] [testng] 05:47:06,891 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bf75dbe - End of configuration. [testng] [2024-12-11 05:47:10,549] [pool-1-thread-7] Initializing /data/stjude/AntoDay4dblmy2GRP.tif: [testng] 05:47:10,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 05:47:10,549 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:47:10,550 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-11_05-47-10.log] [testng] 05:47:10,550 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7874dc53 - End of configuration. [testng] [2024-12-11 05:47:13,468] [pool-1-thread-6] Initializing /data/stjude/Antoday1dblcatsglGRP.tif: [testng] 05:47:13,468 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 05:47:13,468 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:47:13,469 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-11_05-47-13.log] [testng] 05:47:13,469 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3abea866 - End of configuration. [testng] [2024-12-11 05:47:16,099] [pool-1-thread-5] Initializing /data/stjude/AntoDayzerocy3GRP.tif: [testng] 05:47:16,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 05:47:16,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:47:16,100 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-11_05-47-16.log] [testng] 05:47:16,100 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25bf4f1d - End of configuration. [testng] [2024-12-11 05:47:19,074] [pool-1-thread-4] Initializing /data/stjude/AntoDay4dblmyGRP.tif: [testng] 05:47:19,074 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 05:47:19,074 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:47:19,075 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-11_05-47-19.log] [testng] 05:47:19,075 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7039f269 - End of configuration. [testng] [2024-12-11 05:47:21,636] [pool-1-thread-3] Initializing /data/stjude/AntoDayzerocy3OVP.tif: [testng] 05:47:21,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 05:47:21,636 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:47:21,637 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-11_05-47-21.log] [testng] 05:47:21,638 |-INFO in ch.qos.logback.core.sift.SiftProcessor@79ff3d58 - End of configuration. [testng] [2024-12-11 05:47:24,440] [pool-1-thread-2] Initializing /data/brian/Series002_z00_ch00.tif: [testng] 05:47:24,440 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 05:47:24,440 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:47:24,441 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-11_05-47-24.log] [testng] 05:47:24,441 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a66aac - End of configuration. [testng] [2024-12-11 05:47:51,767] [pool-1-thread-4] Initializing /data/dave/series 35/042911_Series035_t00_z000_ch00.tif: [testng] [2024-12-11 05:49:19,773] [pool-1-thread-6] Initializing /data/stjude/AntoDay1cy3/c01f0001.TIF: [testng] [2024-12-11 05:49:21,881] [pool-1-thread-1] Initializing /data/primate/Leica_Image.tif: [testng] 07:49:29,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 07:49:29,140 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 07:49:29,142 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-11_07-49-29.log] [testng] 07:49:29,142 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35b17c06 - 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: 125 minutes 10 seconds Finished: SUCCESS