Package: edgeR

Version: 1.6.15

Command: D:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes --timings edgeR_1.6.15.tar.gz

StartedAt: 2010-10-04 16:36:01 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 16:36:52 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 51.3 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory 'D:/biocbld/bbs-2.6-bioc/meat/edgeR.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'edgeR/DESCRIPTION' ... OK
* this is package 'edgeR' version '1.6.15'
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking tests ...
  Running 'mseq-Tests.R'
 OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* 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
alpha.approxeb	0.19	0.00	0.19
approx.expected.info	0.54	0.00	0.54
calcNormFactors	0.02	0.00	0.02
commonCondLogLikDerDelta	0	0	0
condLogLikDerDelta	0	0	0
condLogLikDerSize	0	0	0
de4DGE	0.06	0.00	0.06
deDGE	0.35	0.00	0.35
equalizeLibSizes	0.17	0.02	0.19
estimateCommonDisp	0.06	0.00	0.06
estimateDispIter	0.47	0.00	0.47
estimatePs	0	0	0
estimateSmoothing	0.04	0.00	0.03
estimateTagwiseDisp	0.2	0.0	0.2
exactTest	0.05	0.00	0.05
findMaxD2	0.34	0.00	0.34
getCounts	0	0	0
interpolateHelper	3.5	0.0	3.5
logLikDerP	0	0	0
maPlot	0.03	0.00	0.03
plotMDS.dge	7.94	0.01	7.97
plotSmear	0.84	0.00	0.84
q2qnbinom	0.14	0.00	0.15
quantileAdjust	0.19	0.00	0.18
readDGE	0	0	0
splitIntoGroups	0	0	0
subsetting	0	0	0
tau2.0.objective	0.01	0.00	0.01
topTags	0.06	0.00	0.07
weightedCondLogLikDerDelta	0	0	0