Package: edgeR

Version: 2.0.5

Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_2.0.5.tar.gz

StartedAt: 2011-04-07 06:04:30 -0700 (Thu, 07 Apr 2011)

EndedAt: 2011-04-07 06:05:24 -0700 (Thu, 07 Apr 2011)

EllapsedTime: 54.6 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/edgeR.Rcheck’
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-unknown-linux-gnu (64-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	0.008	0.000	0.011
approx.expected.info	0.080	0.000	0.083
betaApproxNBTest	0.000	0.000	0.001
calcNormFactors	0.004	0.000	0.003
commonCondLogLikDerDelta	0.004	0.000	0.004
condLogLikDerDelta	0.000	0.000	0.001
condLogLikDerSize	0	0	0
dglmStdResid	0.056	0.000	0.058
dim	0.000	0.000	0.003
equalizeLibSizes	0.156	0.000	0.156
estimateCRDisp	1.716	0.000	1.717
estimateCommonDisp	0.056	0.000	0.057
estimatePs	0.004	0.000	0.007
estimateSmoothing	0.032	0.000	0.032
estimateTagwiseDisp	0.172	0.004	0.173
exactTest	0.048	0.000	0.047
getCounts	0.004	0.000	0.004
glmfit	0.060	0.000	0.057
goodTuring	0.004	0.000	0.005
logLikDerP	0.004	0.000	0.002
maPlot	0.016	0.000	0.015
meanvar	5.392	0.004	5.395
mglm	0.036	0.004	0.038
plotMDS.dge	7.573	0.076	7.662
plotSmear	0.736	0.008	0.743
q2qnbinom	0.116	0.000	0.118
readDGE	0	0	0
splitIntoGroups	0.000	0.000	0.003
subsetting	0.060	0.004	0.063
topTags	0.056	0.000	0.056
weightedComLik	0.032	0.000	0.031
weightedCondLogLikDerDelta	0.004	0.000	0.004