Package: edgeR

Version: 2.3.29

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_2.3.29.tar.gz

StartedAt: 2011-07-07 00:21:13 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 00:22:24 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 71.6 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/edgeR.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* 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 ‘2.3.29’
* 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 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	0.008	0.000	0.012
adjustedProfileLik	0.008	0.000	0.011
approx.expected.info	0.092	0.000	0.092
betaApproxNBTest	0.000	0.000	0.001
bin.dispersion	2.496	0.004	2.502
binomTest	0.000	0.000	0.002
calcNormFactors	0.004	0.000	0.004
commonCondLogLikDerDelta	0.004	0.000	0.004
condLogLikDerDelta	0.000	0.000	0.001
condLogLikDerSize	0.000	0.000	0.001
cpm	0.004	0.000	0.003
cutWithMinN	0.004	0.000	0.003
dglmStdResid	0.06	0.00	0.06
dim	0.004	0.000	0.004
dispBinTrend	0.800	0.004	0.805
dispCoxReid	0.064	0.000	0.065
dispCoxReidInterpolateTagwise	0.28	0.00	0.28
dispCoxReidSplineTrend	1.696	0.000	1.700
equalizeLibSizes	0.172	0.000	0.173
estimateCRDisp	0.696	0.008	0.703
estimateCommonDisp	0.060	0.000	0.062
estimateGLMCommonDisp	0.168	0.000	0.174
estimateGLMTagwiseDisp	1.016	0.000	1.020
estimateGLMTrendedDisp	0.712	0.000	0.711
estimatePs	0.008	0.000	0.006
estimateSmoothing	0.032	0.000	0.035
estimateTagwiseDisp	0.180	0.008	0.194
exactTest	0.052	0.000	0.051
expandAsMatrix	0.004	0.000	0.000
getCounts	0.004	0.000	0.005
getOffset	0.004	0.000	0.003
getPriorN	0.004	0.000	0.003
glmfit	0.544	0.004	0.548
gof	0.04	0.00	0.04
goodTuring	0.008	0.000	0.006
logLikDerP	0.004	0.000	0.003
maPlot	0.016	0.000	0.016
maximizeInterpolant	0.004	0.000	0.002
meanvar	0.368	0.000	0.370
mglm	0.04	0.00	0.04
movingAverageByCol	0.000	0.000	0.001
plotMDS.dge	2.116	0.032	2.223
plotSmear	0.792	0.004	0.826
q2qnbinom	0.176	0.000	0.184
readDGE	0	0	0
splitIntoGroups	0.000	0.000	0.003
subsetting	0.060	0.000	0.063
systematicSubset	0.000	0.000	0.001
thinCounts	0.000	0.000	0.001
topTags	0.064	0.000	0.063
weightedComLik	0.032	0.000	0.031
weightedCondLogLikDerDelta	0.004	0.000	0.004