Started by upstream project "BIOFORMATS-test-repo" build number 273 originally caused by: Started by user devspace 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/jenkins515059428972489313.sh + '[' leica-tcs = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_43102_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 test-automated: [testng] File leak detector installed [testng] 11:48:01,203 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 11:48:01,205 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 11:48:01,205 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:48:01,206 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:48:01,206 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 11:48:01,206 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 11:48:01,206 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 11:48:01,206 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:48:01,207 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:48:01,207 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 11:48:01,207 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:48:01,207 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:48:01,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:48:01,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:48:01,462 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:48:01,462 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:48:01,470 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:48:01,470 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:48:01,470 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:48:01,471 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:48:01,471 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 11:48:01,471 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 11:48:01,472 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 265 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-29 11:48:01,481] [main] java.version = 1.8.0_342 [testng] 11:48:01,485 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:48:01,485 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:48:01,529 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-29_11-48-01.log] [testng] 11:48:01,531 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-29 11:48:01,533] [main] testng.directory = /data [testng] [2024-11-29 11:48:01,533] [main] testng.configDirectory = /config [testng] [2024-11-29 11:48:01,545] [main] testng.multiplier = 1.0 [testng] [2024-11-29 11:48:01,545] [main] testng.in-memory = false [testng] [2024-11-29 11:48:01,545] [main] testng.allow-missing = false [testng] [2024-11-29 11:48:01,545] [main] user.language = en [testng] [2024-11-29 11:48:01,545] [main] user.country = ${user.country} [testng] [2024-11-29 11:48:01,545] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-29 11:48:19,481] [main] ---------------------------------------- [testng] [2024-11-29 11:48:19,481] [main] Total files: 944 [testng] [2024-11-29 11:48:19,481] [main] Scan time: 17.935 s (18 ms/file) [testng] [2024-11-29 11:48:19,481] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-29 11:50:25,226] [pool-1-thread-1] Initializing /data/stjude/AntoDay1dblGRP.tif: [testng] 11:50:25,227 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 11:50:25,227 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:50:25,228 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-29_11-50-25.log] [testng] 11:50:25,228 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3dd72bcc - End of configuration. [testng] [2024-11-29 11:50:27,156] [pool-1-thread-12] Initializing /data/brian/Series002_z01.tif: [testng] 11:50:27,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 11:50:27,156 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:50:27,157 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-29_11-50-27.log] [testng] 11:50:27,157 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75f6ba3d - End of configuration. [testng] [2024-11-29 11:50:29,940] [pool-1-thread-11] Initializing /data/martin/Series028_z00_ch00.tif: [testng] 11:50:29,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 11:50:29,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:50:29,941 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-29_11-50-29.log] [testng] 11:50:29,941 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a750ecc - End of configuration. [testng] [2024-11-29 11:50:32,497] [pool-1-thread-10] Initializing /data/stjude/AntoDay4dblcatdataGRP.tif: [testng] 11:50:32,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 11:50:32,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:50:32,497 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-29_11-50-32.log] [testng] 11:50:32,498 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67caa3c2 - End of configuration. [testng] [2024-11-29 11:50:34,634] [pool-1-thread-9] Initializing /data/stjude/AntoDay1cy3/c01f0001.TIF: [testng] 11:50:34,634 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 11:50:34,634 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:50:34,635 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-29_11-50-34.log] [testng] 11:50:34,635 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a45ed37 - End of configuration. [testng] [2024-11-29 11:50:36,385] [pool-1-thread-8] Initializing /data/stjude/Antoday1dblmysglGRP.tif: [testng] 11:50:36,385 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 11:50:36,385 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:50:36,385 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-29_11-50-36.log] [testng] 11:50:36,386 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e38c04 - End of configuration. [testng] [2024-11-29 11:50:38,286] [pool-1-thread-7] Initializing /data/stjude/Antoday1dblcat2dataGRP.tif: [testng] 11:50:38,286 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 11:50:38,286 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:50:38,287 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-29_11-50-38.log] [testng] 11:50:38,287 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d3d5021 - End of configuration. [testng] [2024-11-29 11:50:40,094] [pool-1-thread-6] Initializing /data/dave/series 35/042911_Series035_t00_z000_ch00.tif: [testng] 11:50:40,094 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 11:50:40,094 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:50:40,095 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-29_11-50-40.log] [testng] 11:50:40,095 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35b5400 - End of configuration. [testng] [2024-11-29 11:51:56,417] [pool-1-thread-5] Initializing /data/stjude/Antoday1dblcatsglGRP.tif: [testng] 11:51:56,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 11:51:56,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:51:56,419 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-29_11-51-56.log] [testng] 11:51:56,419 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75b6bc89 - End of configuration. [testng] [2024-11-29 11:51:58,403] [pool-1-thread-4] Initializing /data/brian/Series002_z00_ch00.tif: [testng] 11:51:58,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 11:51:58,403 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:51:58,403 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-29_11-51-58.log] [testng] 11:51:58,404 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ff045b5 - End of configuration. [testng] [2024-11-29 11:52:00,476] [pool-1-thread-3] Initializing /data/stjude/AntoDay4dblmyGRP.tif: [testng] 11:52:00,476 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 11:52:00,476 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:52:00,476 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-29_11-52-00.log] [testng] 11:52:00,477 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13ae5a1e - End of configuration. [testng] [2024-11-29 11:52:02,417] [pool-1-thread-2] Initializing /data/stjude/AntoDayzerocy3GRP.tif: [testng] 11:52:02,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 11:52:02,417 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:52:02,417 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-29_11-52-02.log] [testng] 11:52:02,418 |-INFO in ch.qos.logback.core.sift.SiftProcessor@580bd9a9 - End of configuration. [testng] [2024-11-29 11:52:18,368] [pool-1-thread-9] Initializing /data/primate/Leica_Image.tif: [testng] [2024-11-29 11:52:25,240] [pool-1-thread-12] Initializing /data/stjude/AntoDayzerocy3OVP.tif: [testng] [2024-11-29 11:52:28,169] [pool-1-thread-8] Initializing /data/stjude/AntoDay4dblmy2GRP.tif: [testng] 13:34:36,737 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 13:34:36,737 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 13:34:36,738 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-29_13-34-36.log] [testng] 13:34:36,739 |-INFO in ch.qos.logback.core.sift.SiftProcessor@181d8899 - 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: 106 minutes 38 seconds Finished: SUCCESS