Package: edgeR

Version: 2.2.6

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_2.2.6.tar.gz

StartedAt: 2011-10-20 12:31:28 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 12:33:02 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 94.1 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/edgeR.Rcheck’
* using R version 2.13.2 (2011-09-30)
* 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 ‘2.2.6’
* checking package namespace 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 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 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 ...
** testing if installed package can be loaded

* DONE (edgeR)

name	user	system	elapsed
DGEList	0.012	0.000	0.013
adjustedProfileLik	0.020	0.000	0.023
approx.expected.info	0.092	0.000	0.090
betaApproxNBTest	0.000	0.000	0.001
bin.dispersion	6.424	0.036	6.515
binomTest	0.004	0.000	0.002
calcNormFactors	0.004	0.000	0.003
commonCondLogLikDerDelta	0.004	0.000	0.004
condLogLikDerDelta	0.004	0.000	0.002
condLogLikDerSize	0	0	0
dglmStdResid	0.064	0.000	0.065
dim	0.000	0.004	0.003
dispBinTrend	3.460	0.000	3.855
dispCoxReid	0.116	0.000	0.116
dispCoxReidInterpolateTagwise	0.392	0.004	0.415
dispCoxReidSplineTrend	4.137	0.000	4.500
equalizeLibSizes	0.172	0.000	0.173
estimateCRDisp	3.528	0.024	3.610
estimateCommonDisp	0.064	0.000	0.065
estimateGLMCommonDisp	0.228	0.000	0.228
estimateGLMTagwiseDisp	4.956	0.004	5.043
estimateGLMTrendedDisp	4.236	0.004	4.262
estimatePs	0.008	0.000	0.007
estimateSmoothing	0.040	0.000	0.036
estimateTagwiseDisp	0.196	0.000	0.194
exactTest	0.052	0.000	0.050
expandAsMatrix	0.000	0.000	0.001
getCounts	0.004	0.000	0.003
getOffsets	0.000	0.000	0.002
glmfit	0.056	0.000	0.059
gof	0.040	0.004	0.041
goodTuring	0.008	0.000	0.006
logLikDerP	0.000	0.000	0.003
maPlot	0.016	0.000	0.016
maximizeInterpolant	0.004	0.000	0.017
meanvar	0.368	0.000	0.378
mglm	0.036	0.000	0.038
movingAverageByCol	0.000	0.000	0.001
plotMDS.dge	8.289	0.076	8.416
plotSmear	0.828	0.016	0.876
q2qnbinom	0.112	0.000	0.111
readDGE	0	0	0
splitIntoGroups	0.000	0.000	0.003
subsetting	0.064	0.000	0.067
systematicSubset	0	0	0
thinCounts	0	0	0
topTags	0.068	0.000	0.068
weightedComLik	0.036	0.000	0.035
weightedCondLogLikDerDelta	0.004	0.000	0.003