BioC 3.4: CHECK report for RUVcorr on morelia

Package: RUVcorr

Version: 1.5.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RUVcorr_1.5.2.tar.gz

StartedAt: 2016-09-20 12:43:29 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 12:44:20 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 51.1 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_1.5.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/RUVcorr.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.5.2’
* 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-3.4-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	0.598	0.015	0.615
PCAPlot	1.608	0.012	1.625
RLEPlot	1.644	0.036	1.681
RUVNaiveRidge	0.494	0.009	0.503
assessQuality	0.117	0.004	0.121
background	0.073	0.001	0.075
calculateThreshold	0.995	0.063	1.058
compareRanks	0.805	0.010	0.815
correlationPlot	0.059	0.004	0.063
eigenvaluePlot	0.225	0.005	0.231
empNegativeControls	0.160	0.001	0.161
findWeights	0.327	0.009	0.337
genePlot	0.241	0.004	0.245
histogramPlot	0.295	0.009	0.304
is.optimizeParameters	0.001	0.000	0.000
is.simulateGEdata	0	0	0
optimizeParameters	1.285	0.025	1.311
plot.optimizeParameters	1.521	0.030	1.552
plotDesign	0.539	0.019	0.639
plotThreshold	1.390	0.059	1.451
print.simulateGEdata	0.000	0.000	0.001
prioritise	0.314	0.011	0.326
simulateGEdata	0.333	0.008	0.341
wcor	0.289	0.011	0.301