Package: RbcBook1

Version: 1.51.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RbcBook1.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RbcBook1_1.51.0.tar.gz

StartedAt: 2019-04-09 03:10:48 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:11:29 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 40.1 seconds

RetCode: 0

Status:  OK

CheckDir: RbcBook1.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RbcBook1.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RbcBook1_1.51.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/RbcBook1.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RbcBook1/DESCRIPTION’ ... OK
* this is package ‘RbcBook1’ version ‘1.51.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RbcBook1’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘graph’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Biobase’ ‘graph’ ‘rpart’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.plotAsGraph: no visible global function definition
  for ‘plot’
bcSweave: no visible global function definition for
  ‘Sweave’
remapAff: no visible binding for global variable
  ‘hgu95av2SYMBOL’
rpart2gNEL: no visible global function definition for
  ‘new’
rpart2gNEL: no visible global function definition for
  ‘edgemode<-’
rpart2gNEL: no visible global function definition for
  ‘addEdge’
Undefined global functions or variables:
  Sweave addEdge edgemode<- hgu95av2SYMBOL new plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("methods", "new")
  importFrom("utils", "Sweave")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: requireAllBook1.Rd:9-10: Dropping empty section \arguments
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/RbcBook1.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RbcBook1
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘RbcBook1’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RbcBook1)

name	user	system	elapsed
bcStangle	0	0	0
bcSweave	0	0	0
bcr	0.720	0.044	0.770
checkVerbatimLines	0.012	0.000	0.012
imageSize	0	0	0
perf	0.002	0.001	0.004
requireAllBook1	0.000	0.000	0.001
rpart2gNEL	0.106	0.004	0.111