Package: RGMQL

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data RGMQL

StartedAt: 2020-04-14 22:48:50 -0400 (Tue, 14 Apr 2020)

EndedAt: 2020-04-14 22:49:37 -0400 (Tue, 14 Apr 2020)

EllapsedTime: 47.0 seconds

RetCode: 1

Status:  ERROR

PackageFile: None

PackageFileSize: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data RGMQL
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* checking for file ‘RGMQL/DESCRIPTION’ ... OK
* preparing ‘RGMQL’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘RGMQL-vignette.Rmd’ using rmarkdown
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
20/04/14 22:49:32 INFO SparkContext: Running Spark version 2.2.0
20/04/14 22:49:33 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
20/04/14 22:49:33 INFO SparkContext: Submitted application: GMQL-R
20/04/14 22:49:33 INFO SecurityManager: Changing view acls to: biocbuild
20/04/14 22:49:33 INFO SecurityManager: Changing modify acls to: biocbuild
20/04/14 22:49:33 INFO SecurityManager: Changing view acls groups to: 
20/04/14 22:49:33 INFO SecurityManager: Changing modify acls groups to: 
20/04/14 22:49:33 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users  with view permissions: Set(biocbuild); groups with view permissions: Set(); users  with modify permissions: Set(biocbuild); groups with modify permissions: Set()
20/04/14 22:49:33 INFO Utils: Successfully started service 'sparkDriver' on port 58319.
20/04/14 22:49:34 INFO SparkEnv: Registering MapOutputTracker
20/04/14 22:49:34 INFO SparkEnv: Registering BlockManagerMaster
20/04/14 22:49:34 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/04/14 22:49:34 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/04/14 22:49:34 INFO DiskBlockManager: Created local directory at /private/var/folders/gs/3s3km1v97wg7qy7rnhs782680000gp/T/blockmgr-a4941664-2f5f-4764-9169-e0341f66a818
20/04/14 22:49:34 INFO MemoryStore: MemoryStore started with capacity 114.6 MB
20/04/14 22:49:34 INFO SparkEnv: Registering OutputCommitCoordinator
20/04/14 22:49:34 INFO Utils: Successfully started service 'SparkUI' on port 4040.
20/04/14 22:49:34 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://208.78.106.115:4040
20/04/14 22:49:34 INFO Executor: Starting executor ID driver on host localhost
20/04/14 22:49:34 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 58320.
20/04/14 22:49:34 INFO NettyBlockTransferService: Server created on 208.78.106.115:58320
20/04/14 22:49:34 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/04/14 22:49:34 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 208.78.106.115, 58320, None)
20/04/14 22:49:34 INFO BlockManagerMasterEndpoint: Registering block manager 208.78.106.115:58320 with 114.6 MB RAM, BlockManagerId(driver, 208.78.106.115, 58320, None)
20/04/14 22:49:34 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 208.78.106.115, 58320, None)
20/04/14 22:49:34 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 208.78.106.115, 58320, None)
GMQL Server is up
Quitting from lines 431-433 (RGMQL-vignette.Rmd) 
Error: processing vignette 'RGMQL-vignette.Rmd' failed with diagnostics:

--- failed re-building ‘RGMQL-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘RGMQL-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted