BioC 3.3: CHECK report for variancePartition on linux2.bioconductor.org

Package: variancePartition

Version: 1.1.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings variancePartition_1.1.0.tar.gz

StartedAt: 2015-10-27 08:48:52 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:51:53 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 180.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: variancePartition.Rcheck

Warnings: 2

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings variancePartition_1.1.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/variancePartition.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (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 ‘1.1.0’
* 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 ... [6s/6s] 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘variancePartition’ for: ‘residuals’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [49s/114s] OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
fitVarPartModel-method         23.004  0.956  38.938
extractVarPart                 11.426  0.451  21.909
residuals-VarParFitList-method  4.914  0.613  11.302
fitExtractVarPartModel-method   0.868  0.199  18.939
sortCols                        0.617  0.336   8.655
plotVarPart                     0.634  0.289   9.013
* 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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.3-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	0.192	0.008	0.199
colinearityScore	0.698	0.003	0.702
extractVarPart	11.426	0.451	21.909
fitExtractVarPartModel-method	0.868	0.199	18.939
fitVarPartModel-method	23.004	0.956	38.938
ggColorHue	0	0	0
plotStratifyBy	0.649	0.080	0.729
plotVarPart	0.634	0.289	9.013
residuals-VarParFitList-method	4.914	0.613	11.302
sortCols	0.617	0.336	8.655