BioC 3.2: CHECK report for variancePartition on perceval

Package: variancePartition

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings variancePartition_1.0.0.tar.gz

StartedAt: 2015-10-27 13:11:01 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 13:15:08 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 247.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: variancePartition.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings variancePartition_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/variancePartition.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘variancePartition/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘variancePartition’ version ‘1.0.0’
* 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 ‘variancePartition’ can be installed ... [9s/9s] 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘getVarianceComponents’
Undocumented S4 methods:
  generic 'plotVarPart' and siglist 'data.frame'
  generic 'plotVarPart' and siglist 'matrix'
  generic 'plotVarPart' and siglist 'varPartResults'
  generic 'sortCols' and siglist 'data.frame'
  generic 'sortCols' and siglist 'matrix'
  generic 'sortCols' and siglist 'varPartResults'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'plotVarPart':
plotVarPart
  Code: function(obj, col = ggColorHue(ncol(obj)), label.angle = 20,
                 ylim = c(0, 100), main = "", ...)
  Docs: function(obj, col, label.angle = 20, ylim = c(0, 100), main =
                 "")
  Argument names in code not in docs:
    ...
  Mismatches in argument default values:
    Name: 'col' Code: ggColorHue(ncol(obj)) Docs: 

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [68s/150s] OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
fitVarPartModel-method         30.866  2.156  46.741
extractVarPart                 16.745  0.955  30.220
residuals-VarParFitList-method  5.846  1.034  14.272
fitExtractVarPartModel-method   1.389  0.104  26.364
sortCols                        0.818  0.037  13.239
plotVarPart                     0.788  0.039  12.238
* 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: 2 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/variancePartition.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
calcVarPart-method	0.199	0.005	0.205
colinearityScore	0.713	0.005	0.718
extractVarPart	16.745	0.955	30.220
fitExtractVarPartModel-method	1.389	0.104	26.364
fitVarPartModel-method	30.866	2.156	46.741
ggColorHue	0.001	0.000	0.001
plotStratifyBy	1.154	0.154	1.309
plotVarPart	0.788	0.039	12.238
residuals-VarParFitList-method	5.846	1.034	14.272
sortCols	0.818	0.037	13.239