BioC 3.5: CHECK report for RUVcorr on veracruz2

Package: RUVcorr

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RUVcorr_1.8.0.tar.gz

StartedAt: 2017-08-16 07:53:32 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 07:54:24 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 51.9 seconds

RetCode: 0

Status:  OK

CheckDir: RUVcorr.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RUVcorr_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RUVcorr.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RUVcorr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RUVcorr’ version ‘1.8.0’
* 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 ‘RUVcorr’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ECDFPlot: no visible global function definition for ‘plot’
ECDFPlot: no visible global function definition for ‘lines’
PCAPlot: no visible global function definition for ‘prcomp’
PCAPlot: no visible global function definition for ‘layout’
PCAPlot: no visible global function definition for ‘par’
PCAPlot: no visible global function definition for ‘plot’
PCAPlot: no visible global function definition for ‘legend’
PCAPlot: no visible global function definition for ‘mtext’
RLEPlot : <anonymous>: no visible global function definition for
  ‘median’
RLEPlot: no visible global function definition for ‘layout’
RLEPlot: no visible global function definition for ‘par’
RLEPlot: no visible global function definition for ‘plot.new’
RLEPlot: no visible global function definition for ‘legend’
RLEPlot: no visible global function definition for ‘mtext’
RLEPlot: no visible global function definition for ‘plot’
RLEPlot: no visible global function definition for ‘boxplot’
RLEPlot: no visible global function definition for ‘abline’
assessQuality: no visible global function definition for ‘cor’
calculateThreshold: no visible global function definition for ‘loess’
compareRanks: no visible global function definition for ‘cor’
correlationPlot: no visible global function definition for ‘mtext’
correlationPlot: no visible global function definition for ‘rect’
eigenvaluePlot: no visible global function definition for ‘plot’
findWeights : <anonymous>: no visible global function definition for
  ‘cor’
findWeights : <anonymous>: no visible global function definition for
  ‘var’
funcThresh: no visible global function definition for ‘cor’
genePlot: no visible global function definition for ‘plot’
genePlot: no visible global function definition for ‘points’
histogramPlot: no visible global function definition for ‘density’
histogramPlot: no visible global function definition for ‘hist’
histogramPlot: no visible global function definition for ‘lines’
histogramPlot : <anonymous>: no visible global function definition for
  ‘density’
mashUp: no visible global function definition for ‘cor’
plot.optimizeParameters : <anonymous>: no visible global function
  definition for ‘xtabs’
plotDesign: no visible global function definition for ‘par’
plotDesign: no visible global function definition for ‘image’
plotThreshold: no visible global function definition for ‘plot’
plotThreshold : <anonymous>: no visible global function definition for
  ‘points’
prioritise: no visible global function definition for ‘cor’
simulateGEdata: no visible global function definition for ‘runif’
simulateGEdata: no visible global function definition for ‘rnorm’
simulateGEdata: no visible global function definition for ‘cor’
wcor : <anonymous>: no visible global function definition for ‘cor’
Undefined global functions or variables:
  abline boxplot cor density hist image layout legend lines loess
  median mtext par plot plot.new points prcomp rect rnorm runif var
  xtabs
Consider adding
  importFrom("graphics", "abline", "boxplot", "hist", "image", "layout",
             "legend", "lines", "mtext", "par", "plot", "plot.new",
             "points", "rect")
  importFrom("stats", "cor", "density", "loess", "median", "prcomp",
             "rnorm", "runif", "var", "xtabs")
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
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/RUVcorr.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
ECDFPlot	0.759	0.022	0.801
PCAPlot	2.027	0.019	2.127
RLEPlot	2.405	0.027	2.532
RUVNaiveRidge	0.538	0.006	0.569
assessQuality	0.104	0.004	0.115
background	0.067	0.002	0.072
calculateThreshold	1.517	0.042	1.618
compareRanks	0.936	0.011	0.971
correlationPlot	0.076	0.005	0.084
eigenvaluePlot	0.328	0.005	0.338
empNegativeControls	0.203	0.002	0.205
findWeights	0.346	0.006	0.364
genePlot	0.230	0.002	0.242
histogramPlot	0.383	0.005	0.391
is.optimizeParameters	0.000	0.001	0.001
is.simulateGEdata	0.001	0.000	0.000
optimizeParameters	1.441	0.024	1.526
plot.optimizeParameters	1.781	0.043	1.893
plotDesign	0.616	0.020	0.670
plotThreshold	1.583	0.039	1.684
print.simulateGEdata	0.000	0.001	0.001
prioritise	0.367	0.007	0.394
simulateGEdata	0.397	0.007	0.421
wcor	0.370	0.011	0.395