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CHECK report for RUVcorr on merida2

This page was generated on 2018-10-17 08:54:36 -0400 (Wed, 17 Oct 2018).

Package 1300/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RUVcorr 1.12.0
Saskia Freytag
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/RUVcorr
Branch: RELEASE_3_7
Last Commit: 9d00e60
Last Changed Date: 2018-04-30 10:35:36 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: RUVcorr
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RUVcorr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RUVcorr_1.12.0.tar.gz
StartedAt: 2018-10-16 23:52:42 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 23:53:34 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 52.4 seconds
RetCode: 0
Status:  OK 
CheckDir: RUVcorr.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RUVcorr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RUVcorr_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/RUVcorr.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.12.0’
* 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 : <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-3.7-bioc/meat/RUVcorr.Rcheck/00check.log’
for details.



Installation output

RUVcorr.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RUVcorr
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘RUVcorr’ ...
** 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
* DONE (RUVcorr)

Tests output


Example timings

RUVcorr.Rcheck/RUVcorr-Ex.timings

nameusersystemelapsed
ECDFPlot0.6800.0340.716
PCAPlot1.7410.0341.789
RLEPlot2.1840.0882.292
RUVNaiveRidge0.4830.0150.504
assessQuality0.0840.0100.095
background0.0750.0060.082
calculateThreshold1.5130.0741.595
compareRanks0.7320.0220.753
correlationPlot0.0780.0020.080
eigenvaluePlot0.2350.0160.253
empNegativeControls0.2590.0200.281
findWeights0.3090.0140.327
genePlot0.2720.0100.285
histogramPlot0.2870.0060.300
is.optimizeParameters0.0000.0000.001
is.simulateGEdata000
optimizeParameters1.5800.0401.639
plot.optimizeParameters1.7190.0651.803
plotDesign0.5330.0260.571
plotThreshold1.6700.0731.761
print.simulateGEdata0.0010.0000.002
prioritise0.4430.0210.471
simulateGEdata0.3590.0170.378
wcor0.4170.0190.442