Package: edgeR

Version: 2.1.12

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch edgeR_2.1.12.tar.gz

StartedAt: 2011-02-24 15:33:47 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 15:34:33 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 46.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: edgeR.Rcheck

Warnings: 3

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/edgeR.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'edgeR/DESCRIPTION' ... OK
* this is package 'edgeR' version '2.1.12'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'edgeR' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
dispCoxReid:
  function(y, design, offset, interval, tol, ...)
dispCoxReid.DGEList:
  function(y, design, offset, interval, tol)

dispCoxReid:
  function(y, design, offset, interval, tol, ...)
dispCoxReid.default:
  function(y, design, offset, interval, tol)

See section 'Generic functions and methods' of the 'Writing R
Extensions' manual.
* 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:
  dispCoxReid dispCoxReid.DGEList dispCoxReid.default getOffsets
  mglmOneGroup.DGEList mglmOneGroup.default
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'mglm':
mglmOneGroup
  Code: function(y, dispersion = 0, offset = NULL, maxit = 50, trace =
                 FALSE)
  Docs: function(y, dispersion = 0, offset = 0, maxit = 50, trace =
                 FALSE)
  Mismatches in argument default values:
    Name: 'offset' Code: NULL Docs: 0

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking data for non-ASCII characters ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'mseq-Tests.R'
 OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 3 warnings, see
  '/Users/biocbuild/bbs-2.8-bioc/meat/edgeR.Rcheck/00check.log'
for details

* installing *source* package 'edgeR' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (edgeR)

name	user	system	elapsed
DGEList	0.013	0.000	0.014
approx.expected.info	0.095	0.000	0.096
betaApproxNBTest	0.001	0.000	0.001
calcNormFactors	0.004	0.000	0.004
commonCondLogLikDerDelta	0.004	0.000	0.004
condLogLikDerDelta	0.002	0.000	0.002
condLogLikDerSize	0	0	0
dglmStdResid	0.064	0.004	0.069
dim	0.003	0.000	0.004
equalizeLibSizes	0.151	0.001	0.152
estimateCRDisp	0.751	0.001	0.752
estimateCommonDisp	0.063	0.000	0.063
estimatePs	0.007	0.000	0.007
estimateSmoothing	0.038	0.002	0.039
estimateTagwiseDisp	0.197	0.005	0.202
exactTest	0.054	0.001	0.054
expandAsMatrix	0	0	0
getCounts	0.004	0.000	0.004
glmfit	0.061	0.002	0.064
goodTuring	0.006	0.000	0.006
logLikDerP	0.003	0.000	0.003
maPlot	0.018	0.001	0.019
meanvar	0.324	0.002	0.326
mglm	0.043	0.001	0.043
plotMDS.dge	7.395	0.475	7.871
plotSmear	0.739	0.016	0.754
q2qnbinom	0.102	0.002	0.105
readDGE	0.001	0.000	0.000
splitIntoGroups	0.003	0.000	0.003
subsetting	0.067	0.001	0.068
topTags	0.060	0.001	0.061
weightedComLik	0.036	0.001	0.036
weightedCondLogLikDerDelta	0.004	0.000	0.004