Package: edgeR

Version: 1.6.15

Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes --timings edgeR_1.6.15.tar.gz

StartedAt: 2010-10-04 16:47:08 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 16:48:08 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 60.9 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/edgeR.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* 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 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 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	0.021	0.002	0.022
alpha.approxeb	0.264	0.002	0.267
approx.expected.info	0.744	0.006	0.753
calcNormFactors	0.005	0.001	0.006
commonCondLogLikDerDelta	0.006	0.000	0.007
condLogLikDerDelta	0.002	0.000	0.003
condLogLikDerSize	0.001	0.000	0.001
de4DGE	0.078	0.001	0.078
deDGE	0.488	0.002	0.495
equalizeLibSizes	0.228	0.088	0.317
estimateCommonDisp	0.090	0.001	0.091
estimateDispIter	0.735	0.006	0.748
estimatePs	0.012	0.000	0.012
estimateSmoothing	0.053	0.000	0.053
estimateTagwiseDisp	0.311	0.012	0.322
exactTest	0.076	0.001	0.077
findMaxD2	0.383	0.017	0.406
getCounts	0.004	0.000	0.005
interpolateHelper	5.054	0.596	5.684
logLikDerP	0.005	0.000	0.005
maPlot	0.027	0.001	0.029
plotMDS.dge	10.750	1.001	11.816
plotSmear	1.133	0.228	1.369
q2qnbinom	0.160	0.050	0.211
quantileAdjust	0.268	0.005	0.275
readDGE	0.001	0.000	0.000
splitIntoGroups	0.005	0.000	0.005
subsetting	0.009	0.001	0.009
tau2.0.objective	0.018	0.001	0.019
topTags	0.101	0.002	0.108
weightedCondLogLikDerDelta	0.006	0.000	0.007