Package: edgeR

Version: 2.1.12

Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings edgeR_2.1.12.tar.gz

StartedAt: 2011-02-24 19:29:47 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 19:30:36 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 48.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: edgeR.Rcheck

Warnings: 3

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/edgeR.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
  'D:/biocbld/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	0.02	0.00	0.01
approx.expected.info	0.09	0.00	0.09
betaApproxNBTest	0	0	0
calcNormFactors	0	0	0
commonCondLogLikDerDelta	0.01	0.00	0.02
condLogLikDerDelta	0	0	0
condLogLikDerSize	0	0	0
dglmStdResid	0.07	0.00	0.06
dim	0	0	0
equalizeLibSizes	0.20	0.00	0.21
estimateCRDisp	0.77	0.00	0.76
estimateCommonDisp	0.06	0.00	0.06
estimatePs	0.01	0.00	0.02
estimateSmoothing	0.04	0.00	0.03
estimateTagwiseDisp	0.18	0.00	0.19
exactTest	0.05	0.00	0.05
expandAsMatrix	0	0	0
getCounts	0.02	0.00	0.01
glmfit	0.06	0.00	0.06
goodTuring	0	0	0
logLikDerP	0	0	0
maPlot	0.03	0.00	0.03
meanvar	0.29	0.01	0.30
mglm	0.04	0.00	0.04
plotMDS.dge	7.52	0.05	7.69
plotSmear	0.81	0.00	0.81
q2qnbinom	0.11	0.00	0.11
readDGE	0	0	0
splitIntoGroups	0.02	0.00	0.02
subsetting	0.06	0.00	0.06
topTags	0.06	0.00	0.06
weightedComLik	0.03	0.00	0.04
weightedCondLogLikDerDelta	0	0	0