Package: RUVcorr

Version: 1.16.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:RUVcorr.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings RUVcorr_1.16.0.tar.gz

StartedAt: 2019-10-16 04:44:38 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:45:24 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 46.4 seconds

RetCode: 0

Status:  OK

CheckDir: RUVcorr.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:RUVcorr.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings RUVcorr_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/RUVcorr.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘1.16.0’
* 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 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 : : 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 : : no visible global function definition for
  ‘cor’
findWeights : : 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 : : no visible global function definition for
  ‘density’
mashUp: no visible global function definition for ‘cor’
plot.optimizeParameters : : 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 : : 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 : : 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 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/RUVcorr.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL RUVcorr
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘RUVcorr’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘RUVcorrVignetteNew.Rnw’ 
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RUVcorr)

name	user	system	elapsed
ECDFPlot	0.928	0.036	0.964
PCAPlot	1.954	0.024	1.977
RLEPlot	1.460	0.008	1.469
RUVNaiveRidge	0.371	0.004	0.375
assessQuality	0.07	0.00	0.07
background	0.060	0.000	0.059
calculateThreshold	1.099	0.000	1.099
compareRanks	0.662	0.007	0.670
correlationPlot	0.071	0.000	0.072
eigenvaluePlot	0.205	0.005	0.210
empNegativeControls	0.139	0.000	0.139
findWeights	0.272	0.000	0.272
genePlot	0.157	0.003	0.161
histogramPlot	0.244	0.001	0.243
is.optimizeParameters	0	0	0
is.simulateGEdata	0	0	0
optimizeParameters	1.239	0.000	1.239
plot.optimizeParameters	2.023	0.000	2.023
plotDesign	0.630	0.003	0.673
plotThreshold	1.387	0.000	1.387
print.simulateGEdata	0	0	0
prioritise	0.424	0.012	0.435
simulateGEdata	0.469	0.000	0.468
wcor	0.523	0.000	0.524