Started by upstream project "BIOFORMATS-test-repo" build number 84
originally caused by:
Started by upstream project "Trigger" build number 95
originally caused by:
Started by user devspace
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/jenkins9455959870990817313.sh
+ '[' bmp = slidebook ']'
++ date +%u
+ '[' 4 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_12790_merge_ci -v /uod/idr/repos/curated/bmp:/data -v /uod/idr-scratch/merge-ci/curated/bmp:/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[javac] warning: [options] source value 8 is obsolete and will be removed in a future release
[javac] warning: [options] target value 8 is obsolete and will be removed in a future release
[javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
[javac] 4 warnings
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] 08:57:28,568 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 08:57:28,569 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service.
[testng] 08:57:28,569 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 08:57:28,570 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 08:57:28,571 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 08:57:28,571 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 08:57:28,571 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 08:57:28,571 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 08:57:28,572 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 08:57:28,573 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 08:57:28,573 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 08:57:28,574 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 08:57:28,751 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 08:57:28,751 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 08:57:28,778 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 08:57:28,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 08:57:28,786 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 08:57:28,786 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 08:57:28,786 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 08:57:28,786 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 08:57:28,787 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration.
[testng] 08:57:28,787 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point
[testng] 08:57:28,787 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 215 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-06-06 08:57:28,797] [main] java.version = 21
[testng] 08:57:28,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 08:57:28,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:57:28,847 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-06_08-57-28.log]
[testng] 08:57:28,850 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration.
[testng] [2024-06-06 08:57:28,852] [main] testng.directory = /data
[testng] [2024-06-06 08:57:28,852] [main] testng.configDirectory = /config
[testng] [2024-06-06 08:57:28,862] [main] testng.multiplier = 1.0
[testng] [2024-06-06 08:57:28,863] [main] testng.in-memory = false
[testng] [2024-06-06 08:57:28,863] [main] testng.allow-missing = false
[testng] [2024-06-06 08:57:28,863] [main] user.language = en
[testng] [2024-06-06 08:57:28,863] [main] user.country = ${user.country}
[testng] [2024-06-06 08:57:28,863] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-06-06 08:57:29,583] [main] ----------------------------------------
[testng] [2024-06-06 08:57:29,583] [main] Total files: 31
[testng] [2024-06-06 08:57:29,583] [main] Scan time: 0.72 s (23 ms/file)
[testng] [2024-06-06 08:57:29,583] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 31 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-06-06 08:57:31,329] [pool-1-thread-1] Initializing /data/curtis/image2.bmp:
[testng] 08:57:31,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 08:57:31,330 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:57:31,331 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-06_08-57-31.log]
[testng] 08:57:31,332 |-INFO in ch.qos.logback.core.sift.SiftProcessor@134d45a2 - End of configuration.
[testng] [2024-06-06 08:57:31,352] [pool-1-thread-12] Initializing /data/dennis/kidney_TFl_Four.bmp:
[testng] 08:57:31,352 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 08:57:31,352 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:57:31,353 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-06_08-57-31.log]
[testng] 08:57:31,354 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45a10322 - End of configuration.
[testng] [2024-06-06 08:57:31,365] [pool-1-thread-11] Initializing /data/brian/images/raw_a_rg.tiff:
[testng] 08:57:31,365 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 08:57:31,365 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:57:31,366 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-06_08-57-31.log]
[testng] 08:57:31,367 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2540d21d - End of configuration.
[testng] [2024-06-06 08:57:31,417] [pool-1-thread-10] Initializing /data/curtis/image3.bmp:
[testng] 08:57:31,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 08:57:31,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:57:31,419 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-06_08-57-31.log]
[testng] 08:57:31,420 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f4606a3 - End of configuration.
[testng] [2024-06-06 08:57:31,430] [pool-1-thread-9] Initializing /data/big-images/6kx6k.bmp:
[testng] 08:57:31,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 08:57:31,430 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:57:31,431 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-06_08-57-31.log]
[testng] 08:57:31,432 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72e2cb2a - End of configuration.
[testng] [2024-06-06 08:57:31,444] [pool-1-thread-8] Initializing /data/dennis/kidney_TFl_Eight.bmp:
[testng] 08:57:31,444 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 08:57:31,444 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:57:31,445 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-06_08-57-31.log]
[testng] 08:57:31,446 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5bb97f3e - End of configuration.
[testng] [2024-06-06 08:57:31,455] [pool-1-thread-7] Initializing /data/frank/cell_mask_error.bmp:
[testng] 08:57:31,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 08:57:31,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:57:31,457 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-06_08-57-31.log]
[testng] 08:57:31,457 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a8bea6f - End of configuration.
[testng] [2024-06-06 08:57:31,466] [pool-1-thread-6] Initializing /data/brian/images/raw_a.bmp:
[testng] 08:57:31,466 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 08:57:31,467 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:57:31,468 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-06_08-57-31.log]
[testng] 08:57:31,469 |-INFO in ch.qos.logback.core.sift.SiftProcessor@380b8202 - End of configuration.
[testng] [2024-06-06 08:57:31,479] [pool-1-thread-5] Initializing /data/stephane/holo0908.bmp:
[testng] 08:57:31,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 08:57:31,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:57:31,481 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-06_08-57-31.log]
[testng] 08:57:31,482 |-INFO in ch.qos.logback.core.sift.SiftProcessor@cc3d36e - End of configuration.
[testng] [2024-06-06 08:57:31,496] [pool-1-thread-4] Initializing /data/dennis/kidney_TFl_Five.bmp:
[testng] 08:57:31,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 08:57:31,497 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:57:31,498 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-06_08-57-31.log]
[testng] 08:57:31,498 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c311bb3 - End of configuration.
[testng] [2024-06-06 08:57:31,513] [pool-1-thread-3] Initializing /data/brian/images/kidney_TFl_1_greyscale.bmp:
[testng] 08:57:31,514 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 08:57:31,514 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:57:31,514 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-06_08-57-31.log]
[testng] 08:57:31,515 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6df5ad27 - End of configuration.
[testng] [2024-06-06 08:57:31,522] [pool-1-thread-2] Initializing /data/brian/images/kidney_TFl_1.bmp:
[testng] 08:57:31,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 08:57:31,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 08:57:31,524 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-06_08-57-31.log]
[testng] 08:57:31,524 |-INFO in ch.qos.logback.core.sift.SiftProcessor@99aaa86 - End of configuration.
[testng] [2024-06-06 08:57:33,325] [pool-1-thread-1] Initializing /data/brian/images/raw_a_rg.bmp:
[testng] [2024-06-06 08:57:33,331] [pool-1-thread-10] Initializing /data/big-images/8kx8k-grey.bmp:
[testng] [2024-06-06 08:57:33,341] [pool-1-thread-3] Initializing /data/dennis/kidney_TFl_Six.bmp:
[testng] [2024-06-06 08:57:33,349] [pool-1-thread-6] Initializing /data/dennis/kidney_TFl_Three.bmp:
[testng] [2024-06-06 08:57:33,356] [pool-1-thread-2] Initializing /data/big-images/6kx6k-grey.bmp:
[testng] [2024-06-06 08:57:33,365] [pool-1-thread-8] Initializing /data/curtis/image4.bmp:
[testng] [2024-06-06 08:57:33,371] [pool-1-thread-7] Initializing /data/bk/100427RBTLPC_FD3__A___5_T_001_ch_00_image_00025_Z_001.bmp:
[testng] [2024-06-06 08:57:33,384] [pool-1-thread-4] Initializing /data/dennis/kidney_TFl_Seven.bmp:
[testng] [2024-06-06 08:57:33,393] [pool-1-thread-12] Initializing /data/brian/images/DMSOHigh_001.bmp:
[testng] [2024-06-06 08:57:33,407] [pool-1-thread-11] Initializing /data/dennis/kidney_TFl_Nine.bmp:
[testng] [2024-06-06 08:57:33,557] [pool-1-thread-5] Initializing /data/curtis/image5.bmp:
[testng] [2024-06-06 08:57:33,662] [pool-1-thread-8] Initializing /data/ticket-12971/foo.bmp:
[testng] [2024-06-06 08:57:33,707] [pool-1-thread-1] Initializing /data/brian/images/23srp5dksub.bmp:
[testng] [2024-06-06 08:57:33,754] [pool-1-thread-5] Initializing /data/bk/ch_00.bmp:
[testng] [2024-06-06 08:57:33,762] [pool-1-thread-3] Initializing /data/big-images/8kx8k.bmp:
[testng] [2024-06-06 08:57:33,771] [pool-1-thread-6] Initializing /data/dennis/kidney_TFl_Two.bmp:
[testng] [2024-06-06 08:57:33,914] [pool-1-thread-11] Initializing /data/curtis/image1.bmp:
[testng] [2024-06-06 08:57:33,953] [pool-1-thread-8] Initializing /data/dennis/kidney_TFl_One.bmp:
[testng] [2024-06-06 08:57:33,960] [pool-1-thread-4] Initializing /data/qa-4538/22577136_Figure 2_A_ATF6 (GST)_13572.bmp:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1643, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 30 seconds
Finished: SUCCESS