Skip to content
[Jenkins]Jenkins
log in

Console Output

Started by upstream project "BIOFORMATS-test-repo" build number 130
originally caused by:
 Started by upstream project "Trigger" build number 147
 originally caused by:
  Started by user devspace
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5
[BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins12298409453114397150.sh
+ '[' scanr = slidebook ']'
++ date +%u
+ '[' 2 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_20435_merge_ci -v /uod/idr/repos/curated/scanr:/data -v /uod/idr-scratch/merge-ci/curated/scanr:/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] 12:05:39,340 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
   [testng] 12:05:39,342 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service.
   [testng] 12:05:39,342 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 12:05:39,343 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
   [testng] 12:05:39,344 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
   [testng] 12:05:39,344 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
   [testng] 12:05:39,344 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
   [testng] 12:05:39,344 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 12:05:39,345 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
   [testng] 12:05:39,346 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
   [testng] 12:05:39,346 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
   [testng] 12:05:39,346 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
   [testng] 12:05:39,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
   [testng] 12:05:39,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
   [testng] 12:05:39,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
   [testng] 12:05:39,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
   [testng] 12:05:39,551 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
   [testng] 12:05:39,551 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
   [testng] 12:05:39,551 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
   [testng] 12:05:39,551 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
   [testng] 12:05:39,552 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration.
   [testng] 12:05:39,553 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point
   [testng] 12:05:39,553 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 208 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
   [testng] [2024-07-23 12:05:39,562] [main] java.version = 11.0.16
   [testng] 12:05:39,565 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
   [testng] 12:05:39,565 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 12:05:39,609 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-07-23_12-05-39.log]
   [testng] 12:05:39,611 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration.
   [testng] [2024-07-23 12:05:39,613] [main] testng.directory = /data
   [testng] [2024-07-23 12:05:39,614] [main] testng.configDirectory = /config
   [testng] [2024-07-23 12:05:39,623] [main] testng.multiplier = 1.0
   [testng] [2024-07-23 12:05:39,625] [main] testng.in-memory = false
   [testng] [2024-07-23 12:05:39,625] [main] testng.allow-missing = false
   [testng] [2024-07-23 12:05:39,625] [main] user.language = en
   [testng] [2024-07-23 12:05:39,625] [main] user.country = ${user.country}
   [testng] [2024-07-23 12:05:39,625] [main] Maximum heap size = 15360 MB
   [testng] Scanning for files...
   [testng] [2024-07-23 12:09:40,599] [main] ----------------------------------------
   [testng] [2024-07-23 12:09:40,600] [main] Total files: 2169
   [testng] [2024-07-23 12:09:40,601] [main] Scan time: 240.974 s (111 ms/file)
   [testng] [2024-07-23 12:09:40,601] [main] ----------------------------------------
   [testng] Building list of tests...
   [testng] Ready to test 17 files
   [testng] [TestNG] Running:
   [testng]   Bio-Formats software test suite
   [testng] 
   [testng] [2024-07-23 12:26:55,106] [pool-1-thread-1] Initializing /data/ruben/12-05-25_009/experiment_descriptor.xml: 
   [testng] 12:26:55,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
   [testng] 12:26:55,107 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 12:26:55,109 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-07-23_12-26-55.log]
   [testng] 12:26:55,110 |-INFO in ch.qos.logback.core.sift.SiftProcessor@df70f0 - End of configuration.
   [testng] [2024-07-23 12:26:55,569] [pool-1-thread-12] Initializing /data/ruben/TestPlate_Mock_01_001/experiment_descriptor.xml: 
   [testng] 12:26:55,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
   [testng] 12:26:55,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 12:26:55,571 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-07-23_12-26-55.log]
   [testng] 12:26:55,571 |-INFO in ch.qos.logback.core.sift.SiftProcessor@297b9abe - End of configuration.
   [testng] [2024-07-23 12:26:55,873] [pool-1-thread-11] Initializing /data/embl/170309_Sec13_GM130m_001/experiment_descriptor.xml: 
   [testng] 12:26:55,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
   [testng] 12:26:55,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 12:26:55,874 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-07-23_12-26-55.log]
   [testng] 12:26:55,874 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18b03250 - End of configuration.
   [testng] [2024-07-23 12:27:05,633] [pool-1-thread-10] Initializing /data/christian/example/experiment_descriptor.xml: 
   [testng] 12:27:05,633 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
   [testng] 12:27:05,633 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 12:27:05,634 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-07-23_12-27-05.log]
   [testng] 12:27:05,635 |-INFO in ch.qos.logback.core.sift.SiftProcessor@460d039f - End of configuration.
   [testng] [2024-07-23 12:27:05,736] [pool-1-thread-9] Initializing /data/embl/Maik_001/experiment_descriptor.xml: 
   [testng] 12:27:05,736 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
   [testng] 12:27:05,736 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 12:27:05,737 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-07-23_12-27-05.log]
   [testng] 12:27:05,738 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1dd73262 - End of configuration.
   [testng] [2024-07-23 12:27:05,893] [pool-1-thread-8] Initializing /data/jcb/201301120/p17/experiment_descriptor.xml: 
   [testng] 12:27:05,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
   [testng] 12:27:05,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 12:27:05,895 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-07-23_12-27-05.log]
   [testng] 12:27:05,895 |-INFO in ch.qos.logback.core.sift.SiftProcessor@34f43095 - End of configuration.
   [testng] [2024-07-23 12:27:14,732] [pool-1-thread-7] Initializing /data/gideon/experiment_descriptor.xml: 
   [testng] 12:27:14,733 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
   [testng] 12:27:14,733 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 12:27:14,734 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-07-23_12-27-14.log]
   [testng] 12:27:14,734 |-INFO in ch.qos.logback.core.sift.SiftProcessor@450312c5 - End of configuration.
   [testng] [2024-07-23 12:27:21,273] [pool-1-thread-6] Initializing /data/ruben/20100827_004/experiment_descriptor.xml: 
   [testng] 12:27:21,273 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
   [testng] 12:27:21,274 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 12:27:21,275 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-07-23_12-27-21.log]
   [testng] 12:27:21,276 |-INFO in ch.qos.logback.core.sift.SiftProcessor@eb3ba8 - End of configuration.
   [testng] [2024-07-23 12:27:23,392] [pool-1-thread-5] Initializing /data/ruben/161009test2/151009_002/experiment_descriptor.xml: 
   [testng] 12:27:23,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
   [testng] 12:27:23,392 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 12:27:23,392 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-07-23_12-27-23.log]
   [testng] 12:27:23,393 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dbbdc7f - End of configuration.
   [testng] [2024-07-23 12:27:26,263] [pool-1-thread-4] Initializing /data/nadine/experiment_descriptor.xml: 
   [testng] 12:27:26,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
   [testng] 12:27:26,263 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 12:27:26,263 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-07-23_12-27-26.log]
   [testng] 12:27:26,264 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36a5f084 - End of configuration.
   [testng] [2024-07-23 12:27:26,293] [pool-1-thread-3] Initializing /data/public/idr0009/0307-10--2007-05-30/experiment_descriptor.xml: 
   [testng] 12:27:26,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
   [testng] 12:27:26,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 12:27:26,294 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-07-23_12-27-26.log]
   [testng] 12:27:26,294 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c5111a9 - End of configuration.
   [testng] [2024-07-23 12:27:27,324] [pool-1-thread-2] Initializing /data/ruben/280809_8wellLT_008/experiment_descriptor.xml: 
   [testng] 12:27:27,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
   [testng] 12:27:27,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
   [testng] 12:27:27,325 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-07-23_12-27-27.log]
   [testng] 12:27:27,325 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62a5b0a - End of configuration.
   [testng] [2024-07-23 12:27:28,267] [pool-1-thread-10] 	testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile)
   [testng] [2024-07-23 12:27:28,468] [pool-1-thread-4] 	testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile)
   [testng] [2024-07-23 12:27:29,856] [pool-1-thread-10] Initializing /data/juergen/Experiment/experiment_descriptor.xml: 
   [testng] [2024-07-23 12:27:29,903] [pool-1-thread-4] Initializing /data/ruben/plate_002/experiment_descriptor.xml: 
   [testng] [2024-07-23 12:27:31,391] [pool-1-thread-10] 	testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile)
   [testng] [2024-07-23 12:27:32,361] [pool-1-thread-10] Initializing /data/ruben/161009test2/151009_001/experiment_descriptor.xml: 
   [testng] [2024-07-23 12:27:40,391] [pool-1-thread-2] 	testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile)
   [testng] [2024-07-23 12:27:40,878] [pool-1-thread-2] Initializing /data/jcb/201301120/p2/experiment_descriptor.xml: 
   [testng] [2024-07-23 12:27:47,961] [pool-1-thread-9] 	testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile)
   [testng] [2024-07-23 12:27:48,016] [pool-1-thread-4] 	testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile)
   [testng] [2024-07-23 12:27:53,346] [pool-1-thread-12] 	testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile)
   [testng] [2024-07-23 12:27:55,981] [pool-1-thread-9] Initializing /data/ruben/scanr_no_labels/Peter/experiment_descriptor.xml: 
   [testng] [2024-07-23 12:28:09,623] [pool-1-thread-1] 	testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile)
   [testng] [2024-07-23 12:28:47,636] [pool-1-thread-7] 	testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile)
   [testng] [2024-07-23 12:30:23,453] [pool-1-thread-3] 	testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile)
   [testng] [2024-07-23 12:30:24,623] [pool-1-thread-9] 	testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile)
   [testng] [2024-07-23 12:30:35,674] [pool-1-thread-11] 	testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile)
   [testng] [2024-07-23 12:31:05,430] [pool-1-thread-5] 	testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile)
   [testng] [2024-07-23 12:31:13,555] [pool-1-thread-6] 	testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile)
   [testng] [2024-07-23 12:31:15,064] [pool-1-thread-8] 	testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile)
   [testng] [2024-07-23 12:31:18,766] [pool-1-thread-10] 	testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile)
   [testng] [2024-07-23 12:31:38,197] [pool-1-thread-2] 	testSaneUsedFiles: FAILED (Used files does not start with getCurrentFile)
   [testng] 
   [testng] ===============================================
   [testng] Bio-Formats software test suite
   [testng] Total tests run: 901, Failures: 17, Skips: 0
   [testng] ===============================================
   [testng] 
   [testng] The tests failed.

BUILD FAILED
/bio-formats-build/bioformats/components/test-suite/build.xml:270: if=failedTest

Total time: 27 minutes 2 seconds
Build step 'Execute shell' marked build as failure
Finished: FAILURE