Package: edgeR

Version: 2.3.25

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch edgeR_2.3.25.tar.gz

StartedAt: 2011-06-22 02:45:13 -0700 (Wed, 22 Jun 2011)

EndedAt: 2011-06-22 02:47:04 -0700 (Wed, 22 Jun 2011)

EllapsedTime: 111.2 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) (2011-06-03 r56037)
* 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 ‘2.3.25’
* 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	0.020	0.002	0.020
adjustedProfileLik	0.028	0.008	0.037
approx.expected.info	0.126	0.001	0.127
betaApproxNBTest	0.001	0.001	0.002
bin.dispersion	3.688	0.016	3.976
binomTest	0.005	0.000	0.010
calcNormFactors	0.005	0.000	0.005
commonCondLogLikDerDelta	0.005	0.000	0.005
condLogLikDerDelta	0.003	0.000	0.003
condLogLikDerSize	0.001	0.000	0.001
cutWithMinN	0.004	0.000	0.004
dglmStdResid	0.078	0.004	0.087
dim	0.005	0.001	0.005
dispBinTrend	6.437	0.031	6.707
dispCoxReid	0.155	0.001	0.157
dispCoxReidInterpolateTagwise	0.544	0.005	0.556
dispCoxReidSplineTrend	5.103	0.020	5.188
equalizeLibSizes	0.227	0.084	0.313
estimateCRDisp	1.533	0.008	1.560
estimateCommonDisp	0.085	0.001	0.085
estimateGLMCommonDisp	0.355	0.001	0.357
estimateGLMTagwiseDisp	1.845	0.011	1.873
estimateGLMTrendedDisp	1.265	0.006	1.284
estimatePs	0.009	0.001	0.010
estimateSmoothing	0.049	0.001	0.057
estimateTagwiseDisp	0.272	0.008	0.282
exactTest	0.068	0.001	0.069
expandAsMatrix	0.001	0.000	0.001
getCounts	0.004	0.000	0.005
getOffsets	0.004	0.000	0.004
getPriorN	0.004	0.000	0.004
glmfit	0.770	0.003	0.778
gof	0.058	0.003	0.062
goodTuring	0.008	0.000	0.010
logLikDerP	0.004	0.001	0.005
maPlot	0.024	0.001	0.026
maximizeInterpolant	0.005	0.000	0.006
meanvar	0.478	0.007	0.490
mglm	0.054	0.001	0.056
movingAverageByCol	0.001	0.000	0.001
plotMDS.dge	2.514	0.491	3.038
plotSmear	1.051	0.216	1.286
q2qnbinom	0.154	0.047	0.202
readDGE	0.000	0.000	0.001
splitIntoGroups	0.005	0.001	0.005
subsetting	0.094	0.004	0.100
systematicSubset	0.001	0.001	0.000
thinCounts	0.001	0.000	0.000
topTags	0.088	0.002	0.090
weightedComLik	0.046	0.000	0.046
weightedCondLogLikDerDelta	0.006	0.000	0.006