Package: edgeR

Version: 2.2.6

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch edgeR_2.2.6.tar.gz

StartedAt: 2011-10-20 14:37:58 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 14:40:13 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 135.0 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/edgeR.Rcheck'
* using R version 2.13.2 (2011-09-30)
* 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 '2.2.6'
* 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 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 ...
** testing if installed package can be loaded

* DONE (edgeR)

name	user	system	elapsed
DGEList	0.018	0.001	0.021
adjustedProfileLik	0.029	0.008	0.038
approx.expected.info	0.127	0.001	0.135
betaApproxNBTest	0.001	0.001	0.001
bin.dispersion	9.336	0.026	9.665
binomTest	0.002	0.001	0.003
calcNormFactors	0.007	0.000	0.007
commonCondLogLikDerDelta	0.006	0.000	0.006
condLogLikDerDelta	0.002	0.000	0.002
condLogLikDerSize	0	0	0
dglmStdResid	0.083	0.005	0.092
dim	0.005	0.000	0.005
dispBinTrend	4.504	0.025	4.562
dispCoxReid	0.150	0.001	0.151
dispCoxReidInterpolateTagwise	0.526	0.004	0.531
dispCoxReidSplineTrend	5.208	0.021	5.538
equalizeLibSizes	0.225	0.086	0.344
estimateCRDisp	4.847	0.016	4.931
estimateCommonDisp	0.085	0.001	0.085
estimateGLMCommonDisp	0.280	0.001	0.281
estimateGLMTagwiseDisp	7.576	0.018	7.637
estimateGLMTrendedDisp	6.862	0.014	6.912
estimatePs	0.009	0.000	0.009
estimateSmoothing	0.048	0.000	0.048
estimateTagwiseDisp	0.267	0.006	0.278
exactTest	0.070	0.000	0.071
expandAsMatrix	0.000	0.000	0.001
getCounts	0.003	0.000	0.003
getOffsets	0.003	0.000	0.003
glmfit	0.072	0.001	0.073
gof	0.052	0.003	0.055
goodTuring	0.008	0.000	0.008
logLikDerP	0.004	0.000	0.004
maPlot	0.024	0.001	0.026
maximizeInterpolant	0.004	0.000	0.005
meanvar	0.429	0.007	0.461
mglm	0.062	0.000	0.071
movingAverageByCol	0.001	0.000	0.001
plotMDS.dge	10.478	0.981	12.105
plotSmear	1.081	0.196	1.305
q2qnbinom	0.161	0.046	0.207
readDGE	0	0	0
splitIntoGroups	0.004	0.000	0.004
subsetting	0.093	0.003	0.096
systematicSubset	0	0	0
thinCounts	0.001	0.000	0.001
topTags	0.087	0.001	0.088
weightedComLik	0.046	0.001	0.049
weightedCondLogLikDerDelta	0.005	0.000	0.005