Package: edgeR

Version: 2.0.5

Command: /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch edgeR_2.0.5.tar.gz

StartedAt: 2011-03-31 05:33:02 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 05:34:32 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 89.7 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.7-bioc/meat/edgeR.Rcheck’
* using R version 2.12.2 Patched (2011-02-25 r54591)
* 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 ‘2.0.5’
* 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 ... 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 ... OK
* checking for code/documentation mismatches ... OK
* 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

* 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	0.021	0.001	0.023
approx.expected.info	0.128	0.002	0.130
betaApproxNBTest	0.001	0.000	0.001
calcNormFactors	0.006	0.001	0.006
commonCondLogLikDerDelta	0.005	0.000	0.006
condLogLikDerDelta	0.002	0.000	0.002
condLogLikDerSize	0.000	0.000	0.001
dglmStdResid	0.086	0.008	0.095
dim	0.004	0.000	0.005
equalizeLibSizes	0.228	0.089	0.325
estimateCRDisp	2.575	0.017	2.611
estimateCommonDisp	0.085	0.001	0.086
estimatePs	0.010	0.001	0.010
estimateSmoothing	0.051	0.000	0.051
estimateTagwiseDisp	0.263	0.006	0.274
exactTest	0.069	0.001	0.072
getCounts	0.003	0.001	0.004
glmfit	0.082	0.001	0.084
goodTuring	0.008	0.001	0.009
logLikDerP	0.005	0.000	0.004
maPlot	0.027	0.002	0.029
meanvar	8.183	0.027	8.268
mglm	0.054	0.002	0.056
plotMDS.dge	10.447	1.025	11.578
plotSmear	1.095	0.207	1.314
q2qnbinom	0.160	0.054	0.222
readDGE	0	0	0
splitIntoGroups	0.005	0.000	0.005
subsetting	0.091	0.003	0.094
topTags	0.084	0.002	0.087
weightedComLik	0.047	0.000	0.047
weightedCondLogLikDerDelta	0.006	0.000	0.006