BioC 3.5: CHECK report for RUVnormalize on toluca2

Package: RUVnormalize

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RUVnormalize_1.9.0.tar.gz

StartedAt: 2017-04-23 09:31:34 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 09:32:21 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 46.7 seconds

RetCode: 0

Status:  OK

CheckDir: RUVnormalize.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RUVnormalize_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RUVnormalize.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RUVnormalize/DESCRIPTION’ ... OK
* this is package ‘RUVnormalize’ version ‘1.9.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘spams’
* 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 ‘RUVnormalize’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘spams’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
iterativeRUV: no visible global function definition for ‘kmeans’
myPalette: no visible global function definition for ‘col2rgb’
myPalette: no visible global function definition for ‘rgb’
svdPlot: no visible global function definition for ‘pdf’
svdPlot: no visible global function definition for ‘par’
svdPlot: no visible global function definition for ‘plot’
svdPlot: no visible global function definition for ‘points’
svdPlot: no visible global function definition for ‘text’
svdPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  col2rgb dev.off kmeans par pdf plot points rgb text
Consider adding
  importFrom("grDevices", "col2rgb", "dev.off", "pdf", "rgb")
  importFrom("graphics", "par", "plot", "points", "text")
  importFrom("stats", "kmeans")
to your NAMESPACE file.
* checking Rd files ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
clScore 5.107  0.183   5.306
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/RUVnormalize.Rcheck/00check.log’
for details.

* installing *source* package ‘RUVnormalize’ ...
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RUVnormalize)

name	user	system	elapsed
clScore	5.107	0.183	5.306
iterativeRUV	0.148	0.003	0.151
naiveRandRUV	4.613	0.159	4.782
naiveReplicateRUV	3.193	0.215	3.416
svdPlot	4.589	0.193	4.791