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BioC 3.6: CHECK report for RUVcorr on malbec1

This page was generated on 2017-08-16 13:23:08 -0400 (Wed, 16 Aug 2017).

Package 1188/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RUVcorr 1.9.0
Saskia Freytag
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RUVcorr
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RUVcorr
Version: 1.9.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings RUVcorr_1.9.0.tar.gz
StartedAt: 2017-08-16 02:12:59 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:13:40 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 41.3 seconds
RetCode: 0
Status:  OK 
CheckDir: RUVcorr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings RUVcorr_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/RUVcorr.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.9.0’
* 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 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-3.6-bioc/meat/RUVcorr.Rcheck/00check.log’
for details.


RUVcorr.Rcheck/00install.out:

* 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)

RUVcorr.Rcheck/RUVcorr-Ex.timings:

nameusersystemelapsed
ECDFPlot0.7960.0120.810
PCAPlot1.6640.0041.670
RLEPlot1.7960.0041.798
RUVNaiveRidge0.3680.0000.369
assessQuality0.1480.0040.150
background0.0600.0000.059
calculateThreshold1.1640.0001.164
compareRanks0.6680.0040.671
correlationPlot0.0680.0000.070
eigenvaluePlot0.2200.0000.221
empNegativeControls0.2480.0000.247
findWeights0.3600.0000.358
genePlot0.2120.0000.212
histogramPlot0.3400.0000.339
is.optimizeParameters0.0000.0000.001
is.simulateGEdata000
optimizeParameters1.2800.0001.281
plot.optimizeParameters1.5720.0001.573
plotDesign0.6480.0120.714
plotThreshold1.2320.0121.242
print.simulateGEdata000
prioritise0.3880.0000.387
simulateGEdata0.4200.0000.421
wcor0.3920.0040.393