Started by upstream project "BIOFORMATS-test-repo" build number 289
originally caused by:
Started by upstream project "Trigger" build number 308
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/jenkins4993293119446982956.sh
+ '[' gatan-dm2 = slidebook ']'
++ date +%u
+ '[' 5 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_45652_merge_ci -v /uod/idr/repos/curated/gatan-dm2:/data -v /uod/idr-scratch/merge-ci/curated/gatan-dm2:/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] 02:38:46,318 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 02:38:46,319 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service.
[testng] 02:38:46,319 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:38:46,320 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 02:38:46,321 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 02:38:46,321 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 02:38:46,321 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 02:38:46,321 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:38:46,321 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 02:38:46,322 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 02:38:46,322 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 02:38:46,322 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 02:38:46,536 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 02:38:46,536 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 02:38:46,562 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 02:38:46,562 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 02:38:46,570 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 02:38:46,570 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 02:38:46,570 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 02:38:46,571 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 02:38:46,571 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration.
[testng] 02:38:46,572 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point
[testng] 02:38:46,572 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 251 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-12-13 02:38:46,581] [main] java.version = 1.8.0_342
[testng] 02:38:46,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 02:38:46,585 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:38:46,628 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-13_02-38-46.log]
[testng] 02:38:46,629 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration.
[testng] [2024-12-13 02:38:46,631] [main] testng.directory = /data
[testng] [2024-12-13 02:38:46,631] [main] testng.configDirectory = /config
[testng] [2024-12-13 02:38:46,643] [main] testng.multiplier = 1.0
[testng] [2024-12-13 02:38:46,643] [main] testng.in-memory = false
[testng] [2024-12-13 02:38:46,643] [main] testng.allow-missing = false
[testng] [2024-12-13 02:38:46,643] [main] user.language = en
[testng] [2024-12-13 02:38:46,643] [main] user.country = ${user.country}
[testng] [2024-12-13 02:38:46,643] [main] Maximum heap size = 13653 MB
[testng] Scanning for files...
[testng] [2024-12-13 02:39:13,850] [main] ----------------------------------------
[testng] [2024-12-13 02:39:13,850] [main] Total files: 25
[testng] [2024-12-13 02:39:13,851] [main] Scan time: 27.207 s (1088 ms/file)
[testng] [2024-12-13 02:39:13,851] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 18 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-12-13 02:39:48,108] [pool-1-thread-1] Initializing /data/imagic/1-1.dm2:
[testng] 02:39:48,109 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 02:39:48,109 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:39:48,110 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-13_02-39-48.log]
[testng] 02:39:48,110 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7907742d - End of configuration.
[testng] [2024-12-13 02:39:48,896] [pool-1-thread-12] Initializing /data/pang/screen capture of metadata/tem_dm_microscope_info.png:
[testng] 02:39:48,897 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 02:39:48,897 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:39:48,898 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-13_02-39-48.log]
[testng] 02:39:48,898 |-INFO in ch.qos.logback.core.sift.SiftProcessor@380ddaa1 - End of configuration.
[testng] [2024-12-13 02:39:49,016] [pool-1-thread-11] Initializing /data/imagic/not read correctly/Abeta Moon.dm2:
[testng] 02:39:49,016 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 02:39:49,016 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:39:49,017 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-13_02-39-49.log]
[testng] 02:39:49,017 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6015eb94 - End of configuration.
[testng] [2024-12-13 02:39:49,610] [pool-1-thread-10] Initializing /data/imagic/TEM 10118.dm2:
[testng] 02:39:49,610 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 02:39:49,610 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:39:49,611 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-13_02-39-49.log]
[testng] 02:39:49,611 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37f3aef6 - End of configuration.
[testng] [2024-12-13 02:39:50,136] [pool-1-thread-9] Initializing /data/pang/unproc-auto:
[testng] 02:39:50,137 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 02:39:50,137 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:39:50,138 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-13_02-39-50.log]
[testng] 02:39:50,138 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2705cb8e - End of configuration.
[testng] [2024-12-13 02:39:50,713] [pool-1-thread-8] Initializing /data/pang/grating025k.dm2:
[testng] 02:39:50,713 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 02:39:50,713 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:39:50,714 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-13_02-39-50.log]
[testng] 02:39:50,715 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a094265 - End of configuration.
[testng] [2024-12-13 02:39:51,335] [pool-1-thread-7] Initializing /data/pang/screen capture of metadata/tem_dm_tags_info2.png:
[testng] 02:39:51,335 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 02:39:51,335 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:39:51,336 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-13_02-39-51.log]
[testng] 02:39:51,336 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c4bd7f4 - End of configuration.
[testng] [2024-12-13 02:39:51,450] [pool-1-thread-6] Initializing /data/pang/DLMeD2E1_010500x03.dm2:
[testng] 02:39:51,450 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 02:39:51,450 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:39:51,451 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-13_02-39-51.log]
[testng] 02:39:51,451 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4aacd6c7 - End of configuration.
[testng] [2024-12-13 02:39:52,101] [pool-1-thread-5] Initializing /data/pang/10500x-o4:
[testng] 02:39:52,101 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 02:39:52,101 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:39:52,102 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-13_02-39-52.log]
[testng] 02:39:52,103 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f962faf - End of configuration.
[testng] [2024-12-13 02:39:52,820] [pool-1-thread-4] Initializing /data/pang/screen capture of metadata/tem_dm_tags_info1.png:
[testng] 02:39:52,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 02:39:52,821 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:39:52,821 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-13_02-39-52.log]
[testng] 02:39:52,822 |-INFO in ch.qos.logback.core.sift.SiftProcessor@585baae7 - End of configuration.
[testng] [2024-12-13 02:39:52,924] [pool-1-thread-3] Initializing /data/pang/screen capture of metadata/tem_dm_keywords_info.png:
[testng] 02:39:52,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 02:39:52,924 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:39:52,925 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-13_02-39-52.log]
[testng] 02:39:52,925 |-INFO in ch.qos.logback.core.sift.SiftProcessor@223d02da - End of configuration.
[testng] [2024-12-13 02:39:53,047] [pool-1-thread-2] Initializing /data/imagic/not read correctly/Zucchini_preview.png:
[testng] 02:39:53,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 02:39:53,048 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 02:39:53,049 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-13_02-39-53.log]
[testng] 02:39:53,049 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1914ad7c - End of configuration.
[testng] [2024-12-13 02:39:58,636] [pool-1-thread-3] Initializing /data/imagic/not read correctly/Zucchini.dm2:
[testng] [2024-12-13 02:39:59,453] [pool-1-thread-12] Initializing /data/pang/screen capture of metadata/tem_dm_general_info.png:
[testng] [2024-12-13 02:39:59,556] [pool-1-thread-4] Initializing /data/imagic/Histiocyte in Skin Dermis.dm2:
[testng] [2024-12-13 02:40:00,294] [pool-1-thread-2] Initializing /data/imagic/13008.dm2:
[testng] [2024-12-13 02:40:01,057] [pool-1-thread-7] Initializing /data/imagic/not read correctly/Abeta Moon_preview.png:
[testng] [2024-12-13 02:40:02,790] [pool-1-thread-11] Initializing /data/pang/signed:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 954, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 1 minute 27 seconds
Finished: SUCCESS