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 19:04:04 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 19:05:06 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 62.2 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: UTF-8
* 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	0.019	0.001	0.020
approx.expected.info	0.128	0.001	0.130
betaApproxNBTest	0.001	0.000	0.002
calcNormFactors	0.005	0.001	0.006
commonCondLogLikDerDelta	0.005	0.000	0.006
condLogLikDerDelta	0.002	0.001	0.002
condLogLikDerSize	0.001	0.000	0.001
dglmStdResid	0.087	0.009	0.096
dim	0.005	0.000	0.005
equalizeLibSizes	0.243	0.071	0.321
estimateCRDisp	1.013	0.004	1.027
estimateCommonDisp	0.084	0.000	0.084
estimatePs	0.010	0.001	0.010
estimateSmoothing	0.049	0.000	0.050
estimateTagwiseDisp	0.260	0.006	0.267
exactTest	0.072	0.001	0.072
expandAsMatrix	0.001	0.000	0.001
getCounts	0.004	0.000	0.004
glmfit	0.087	0.001	0.088
goodTuring	0.008	0.001	0.009
logLikDerP	0.004	0.000	0.005
maPlot	0.025	0.001	0.027
meanvar	0.440	0.006	0.446
mglm	0.060	0.001	0.060
plotMDS.dge	10.561	1.031	11.655
plotSmear	1.090	0.224	1.324
q2qnbinom	0.159	0.048	0.207
readDGE	0.000	0.000	0.001
splitIntoGroups	0.005	0.000	0.005
subsetting	0.097	0.002	0.100
topTags	0.091	0.002	0.093
weightedComLik	0.049	0.000	0.050
weightedCondLogLikDerDelta	0.005	0.000	0.005