Package: edgeR

Version: 2.0.5

Command: E:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings edgeR_2.0.5.tar.gz

StartedAt: 2011-03-31 06:19:01 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 06:20:24 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 83.3 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.7-bioc/meat/edgeR.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 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	0.02	0.00	0.02
approx.expected.info	0.12	0.00	0.12
betaApproxNBTest	0	0	0
calcNormFactors	0	0	0
commonCondLogLikDerDelta	0	0	0
condLogLikDerDelta	0.02	0.00	0.02
condLogLikDerSize	0	0	0
dglmStdResid	0.06	0.01	0.09
dim	0	0	0
equalizeLibSizes	0.15	0.00	0.15
estimateCRDisp	2.59	0.00	2.61
estimateCommonDisp	0.08	0.00	0.08
estimatePs	0.01	0.00	0.01
estimateSmoothing	0.05	0.00	0.05
estimateTagwiseDisp	0.24	0.00	0.23
exactTest	0.07	0.00	0.08
getCounts	0	0	0
glmfit	0.08	0.00	0.08
goodTuring	0.02	0.00	0.02
logLikDerP	0	0	0
maPlot	0.08	0.00	0.07
meanvar	8.48	0.02	8.52
mglm	0.05	0.00	0.05
plotMDS.dge	14.77	0.03	14.88
plotSmear	1.14	0.00	1.14
q2qnbinom	0.14	0.00	0.14
readDGE	0	0	0
splitIntoGroups	0	0	0
subsetting	0.09	0.00	0.09
topTags	0.1	0.0	0.1
weightedComLik	0.04	0.00	0.04
weightedCondLogLikDerDelta	0	0	0