Package: edgeR

Version: 2.3.13

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch edgeR_2.3.13.tar.gz

StartedAt: 2011-05-09 14:19:34 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 14:21:49 -0700 (Mon, 09 May 2011)

EllapsedTime: 135.8 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/edgeR.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* 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 ‘2.3.13’
* 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 installed package size ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘edgeR-Tests.R’
  Comparing ‘edgeR-Tests.Rout’ to ‘edgeR-Tests.Rout.save’ ... OK
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... 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 ...
*** tangling vignette sources ...
   ‘edgeR.Rnw’ 
** testing if installed package can be loaded

* DONE (edgeR)

name	user	system	elapsed
DGEList	0.019	0.001	0.021
adjustedProfileLik	0.028	0.008	0.043
approx.expected.info	0.125	0.001	0.126
betaApproxNBTest	0.001	0.000	0.001
bin.dispersion	9.348	0.031	9.762
binomTest	0.003	0.001	0.003
calcNormFactors	0.005	0.000	0.005
commonCondLogLikDerDelta	0.006	0.000	0.006
condLogLikDerDelta	0.003	0.000	0.002
condLogLikDerSize	0.001	0.000	0.001
cutWithMinN	0.005	0.000	0.006
dglmStdResid	0.080	0.005	0.085
dim	0.005	0.000	0.005
dispBinTrend	4.545	0.026	4.829
dispCoxReid	0.150	0.001	0.152
dispCoxReidInterpolateTagwise	0.523	0.004	0.533
dispCoxReidSplineTrend	5.138	0.015	5.217
equalizeLibSizes	0.227	0.078	0.312
estimateCRDisp	4.810	0.013	4.858
estimateCommonDisp	0.088	0.000	0.088
estimateGLMCommonDisp	0.333	0.001	0.335
estimateGLMTagwiseDisp	7.585	0.019	7.655
estimateGLMTrendedDisp	6.888	0.018	7.117
estimatePs	0.010	0.001	0.012
estimateSmoothing	0.049	0.001	0.054
estimateTagwiseDisp	0.259	0.006	0.265
exactTest	0.072	0.001	0.073
expandAsMatrix	0.001	0.000	0.001
getCounts	0.004	0.000	0.004
getOffsets	0.004	0.000	0.004
getPriorN	0.004	0.001	0.004
glmfit	0.076	0.001	0.077
gof	0.055	0.003	0.057
goodTuring	0.009	0.001	0.009
logLikDerP	0.004	0.000	0.004
maPlot	0.023	0.001	0.025
maximizeInterpolant	0.002	0.001	0.003
meanvar	0.422	0.006	0.429
mglm	0.061	0.001	0.062
movingAverageByCol	0.001	0.001	0.002
plotMDS.dge	10.542	0.968	11.998
plotSmear	1.081	0.207	1.456
q2qnbinom	0.166	0.054	0.324
readDGE	0.000	0.000	0.001
splitIntoGroups	0.005	0.000	0.005
subsetting	0.096	0.003	0.120
systematicSubset	0.001	0.000	0.000
thinCounts	0	0	0
topTags	0.092	0.002	0.103
weightedComLik	0.046	0.000	0.048
weightedCondLogLikDerDelta	0.005	0.000	0.006