Package: edgeR

Version: 2.4.6

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch edgeR_2.4.6.tar.gz

StartedAt: 2012-03-24 00:47:33 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 00:49:07 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 94.6 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 2.14.2 (2012-02-29)
* 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 '2.4.6'
* 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 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	0.026	0.002	0.028
adjustedProfileLik	0.016	0.003	0.020
approx.expected.info	0.146	0.005	0.160
betaApproxNBTest	0.001	0.000	0.001
bin.dispersion	2.599	0.015	2.645
binomTest	0.002	0.001	0.003
calcNormFactors	0.005	0.000	0.005
commonCondLogLikDerDelta	0.004	0.000	0.004
condLogLikDerDelta	0.001	0.000	0.002
condLogLikDerSize	0.000	0.001	0.000
cpm	0.003	0.000	0.003
cutWithMinN	0.003	0.000	0.003
dglmStdResid	0.078	0.004	0.083
dim	0.004	0.000	0.004
dispBinTrend	0.940	0.009	0.967
dispCoxReid	0.071	0.001	0.072
dispCoxReidInterpolateTagwise	0.263	0.003	0.267
dispCoxReidSplineTrend	1.944	0.008	1.965
equalizeLibSizes	0.271	0.078	0.350
estimateCommonDisp	0.075	0.002	0.078
estimateExonGenewisedisp	0.109	0.000	0.109
estimateGLMCommonDisp	0.206	0.001	0.211
estimateGLMTagwiseDisp	1.113	0.005	1.121
estimateGLMTrendedDisp	0.821	0.003	0.824
estimatePs	0.009	0.000	0.010
estimateSmoothing	0.039	0.000	0.040
estimateTagwiseDisp	0.319	0.015	0.335
exactTest	0.113	0.002	0.116
expandAsMatrix	0.001	0.000	0.000
getCounts	0.036	0.001	0.036
getPriorN	0.003	0.001	0.003
glmfit	0.777	0.003	0.780
gof	0.045	0.003	0.049
goodTuring	0.013	0.001	0.015
logLikDerP	0.003	0.000	0.003
maPlot	0.030	0.003	0.033
maximizeInterpolant	0.004	0.001	0.005
meanvar	0.361	0.018	0.380
mglm	0.051	0.001	0.053
movingAverageByCol	0.001	0.000	0.001
plotExonUsage	0.011	0.001	0.013
plotMDS.dge	0.020	0.003	0.023
plotSmear	0.972	0.189	1.344
q2qnbinom	0.210	0.049	0.285
readDGE	0	0	0
spliceVariants	0.035	0.000	0.036
splitIntoGroups	0.004	0.001	0.003
subsetting	0.066	0.002	0.072
systematicSubset	0.000	0.001	0.000
thinCounts	0.000	0.000	0.001
topTags	0.055	0.002	0.113
weightedComLik	0.038	0.000	0.047
weightedCondLogLikDerDelta	0.005	0.000	0.007