Package: edgeR

Version: 2.7.16

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch edgeR_2.7.16.tar.gz

StartedAt: 2012-06-20 23:30:26 -0700 (Wed, 20 Jun 2012)

EndedAt: 2012-06-20 23:32:19 -0700 (Wed, 20 Jun 2012)

EllapsedTime: 113.1 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/edgeR.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'edgeR/DESCRIPTION' ... OK
* this is package 'edgeR' version '2.7.16'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 installed files from '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
** installing vignettes
   'edgeR.Rnw' 
** testing if installed package can be loaded

* DONE (edgeR)

name	user	system	elapsed
DGEList	0.033	0.004	0.039
adjustedProfileLik	0.021	0.003	0.024
bin.dispersion	2.913	0.014	2.945
binomTest	0.003	0.000	0.003
calcNormFactors	0.011	0.000	0.012
commonCondLogLikDerDelta	0.003	0.000	0.004
condLogLikDerSize	0.001	0.000	0.001
cpm	0.004	0.001	0.003
cutWithMinN	0.003	0.000	0.003
dglmStdResid	0.077	0.006	0.088
dim	0.003	0.001	0.004
dispBinTrend	1.737	0.011	1.762
dispCoxReid	0.136	0.000	0.137
dispCoxReidInterpolateTagwise	0.331	0.003	0.337
dispCoxReidSplineTrend	3.558	0.011	3.591
equalizeLibSizes	0.052	0.011	0.063
estimateCommonDisp	0.060	0.001	0.062
estimateExonGenewisedisp	0.054	0.000	0.055
estimateGLMCommonDisp	0.310	0.001	0.316
estimateGLMTagwiseDisp	1.864	0.006	1.882
estimateGLMTrendedDisp	1.514	0.005	1.527
estimatePs	0.008	0.000	0.008
estimateTagwiseDisp	0.259	0.005	0.264
estimateTrendedDisp	1.978	0.091	2.088
exactTest	0.063	0.001	0.065
expandAsMatrix	0	0	0
getCounts	0.026	0.001	0.027
getPriorN	0.003	0.000	0.003
glmfit	1.446	0.005	1.457
gof	0.079	0.003	0.082
goodTuring	0.008	0.001	0.010
locallyWeightedMean	0.006	0.001	0.007
logLikDerP	0.003	0.001	0.004
maPlot	0.033	0.003	0.036
maximizeInterpolant	0.002	0.000	0.001
maximizeQuadratic	0.002	0.000	0.001
meanvar	0.317	0.006	0.323
mglm	0.060	0.001	0.062
movingAverageByCol	0.000	0.001	0.001
plotBCV	2.220	0.097	2.350
plotExonUsage	0.013	0.002	0.014
plotMDS.dge	0.022	0.005	0.028
plotSmear	0.976	0.189	1.209
predFC	0.213	0.004	0.217
q2qnbinom	0.173	0.052	0.227
readDGE	0	0	0
spliceVariants	0.056	0.000	0.058
splitIntoGroups	0.004	0.000	0.004
subsetting	0.067	0.002	0.069
systematicSubset	0.001	0.000	0.000
thinCounts	0.000	0.001	0.001
topTags	0.050	0.001	0.054
weightedCondLogLikDerDelta	0.005	0.000	0.006
zscoreNBinom	0.001	0.000	0.000