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Started by upstream project "BIOFORMATS-test-repo" build number 274 originally caused by: Started by upstream project "Trigger" build number 295 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins5431140418433979852.sh + '[' leica-tcs = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_43266_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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 03:33:59,469 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:33:59,471 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 03:33:59,471 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:33:59,472 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:33:59,473 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:33:59,473 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:33:59,474 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 03:33:59,474 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:33:59,474 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:33:59,475 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:33:59,475 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:33:59,476 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:33:59,644 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:33:59,644 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:33:59,665 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:33:59,665 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:33:59,671 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:33:59,671 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:33:59,671 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:33:59,671 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:33:59,671 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 03:33:59,672 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 03:33:59,672 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 198 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-30 03:33:59,681] [main] java.version = 11.0.16 [testng] 03:33:59,684 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:33:59,684 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:33:59,725 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-30_03-33-59.log] [testng] 03:33:59,726 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-11-30 03:33:59,728] [main] testng.directory = /data [testng] [2024-11-30 03:33:59,728] [main] testng.configDirectory = /config [testng] [2024-11-30 03:33:59,737] [main] testng.multiplier = 1.0 [testng] [2024-11-30 03:33:59,738] [main] testng.in-memory = false [testng] [2024-11-30 03:33:59,739] [main] testng.allow-missing = false [testng] [2024-11-30 03:33:59,739] [main] user.language = en [testng] [2024-11-30 03:33:59,739] [main] user.country = ${user.country} [testng] [2024-11-30 03:33:59,739] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-30 03:34:29,529] [main] ---------------------------------------- [testng] [2024-11-30 03:34:29,529] [main] Total files: 944 [testng] [2024-11-30 03:34:29,529] [main] Scan time: 29.79 s (31 ms/file) [testng] [2024-11-30 03:34:29,529] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 15 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-30 03:35:59,072] [pool-1-thread-1] Initializing /data/stjude/AntoDayzerocy3OVP.tif: [testng] 03:35:59,073 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:35:59,073 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:35:59,075 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-30_03-35-59.log] [testng] 03:35:59,075 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20d8eaeb - End of configuration. [testng] [2024-11-30 03:36:00,468] [pool-1-thread-12] Initializing /data/stjude/AntoDay1cy3/c01f0001.TIF: [testng] 03:36:00,468 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:36:00,469 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:36:00,469 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-30_03-36-00.log] [testng] 03:36:00,470 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52bd2426 - End of configuration. [testng] [2024-11-30 03:36:01,591] [pool-1-thread-11] Initializing /data/stjude/AntoDay4dblmy2GRP.tif: [testng] 03:36:01,591 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:36:01,591 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:36:01,591 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-30_03-36-01.log] [testng] 03:36:01,592 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13d5ffba - End of configuration. [testng] [2024-11-30 03:36:02,940] [pool-1-thread-10] Initializing /data/stjude/AntoDayzerocy3GRP.tif: [testng] 03:36:02,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:36:02,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:36:02,941 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-30_03-36-02.log] [testng] 03:36:02,942 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b424a48 - End of configuration. [testng] [2024-11-30 03:36:04,273] [pool-1-thread-9] Initializing /data/primate/Leica_Image.tif: [testng] 03:36:04,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:36:04,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:36:04,274 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-30_03-36-04.log] [testng] 03:36:04,274 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68f8ee92 - End of configuration. [testng] [2024-11-30 03:36:05,449] [pool-1-thread-8] Initializing /data/stjude/Antoday1dblcatsglGRP.tif: [testng] 03:36:05,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:36:05,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:36:05,450 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-30_03-36-05.log] [testng] 03:36:05,450 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55b5d3e4 - End of configuration. [testng] [2024-11-30 03:36:06,663] [pool-1-thread-7] Initializing /data/stjude/Antoday1dblcat2dataGRP.tif: [testng] 03:36:06,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:36:06,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:36:06,664 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-30_03-36-06.log] [testng] 03:36:06,664 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4476e930 - End of configuration. [testng] [2024-11-30 03:36:07,836] [pool-1-thread-6] Initializing /data/brian/Series002_z01.tif: [testng] 03:36:07,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:36:07,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:36:07,837 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-30_03-36-07.log] [testng] 03:36:07,837 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19acc3b5 - End of configuration. [testng] [2024-11-30 03:36:09,663] [pool-1-thread-5] Initializing /data/martin/Series028_z00_ch00.tif: [testng] 03:36:09,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:36:09,663 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:36:09,664 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-30_03-36-09.log] [testng] 03:36:09,664 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55799e93 - End of configuration. [testng] [2024-11-30 03:36:11,361] [pool-1-thread-4] Initializing /data/stjude/AntoDay1dblGRP.tif: [testng] 03:36:11,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:36:11,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:36:11,362 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-30_03-36-11.log] [testng] 03:36:11,362 |-INFO in ch.qos.logback.core.sift.SiftProcessor@67e18eba - End of configuration. [testng] [2024-11-30 03:36:12,575] [pool-1-thread-3] Initializing /data/dave/series 35/042911_Series035_t00_z000_ch00.tif: [testng] 03:36:12,575 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:36:12,575 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:36:12,576 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-30_03-36-12.log] [testng] 03:36:12,576 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7cf7f0a1 - End of configuration. [testng] [2024-11-30 03:37:01,703] [pool-1-thread-2] Initializing /data/brian/Series002_z00_ch00.tif: [testng] 03:37:01,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:37:01,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:37:01,703 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-30_03-37-01.log] [testng] 03:37:01,714 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d2bd71e - End of configuration. [testng] [2024-11-30 03:37:11,806] [pool-1-thread-12] Initializing /data/stjude/AntoDay4dblcatdataGRP.tif: [testng] [2024-11-30 03:37:13,670] [pool-1-thread-9] Initializing /data/stjude/AntoDay4dblmyGRP.tif: [testng] [2024-11-30 03:37:16,817] [pool-1-thread-6] Initializing /data/stjude/Antoday1dblmysglGRP.tif: [testng] 04:43:48,743 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:43:48,743 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:43:48,744 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-30_04-43-48.log] [testng] 04:43:48,745 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a17b2e3 - 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: 69 minutes 54 seconds Finished: SUCCESS