Package: DEXSeq

Version: 1.3.2

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DEXSeq_1.3.2.tar.gz

StartedAt: 2012-06-20 23:19:09 -0700 (Wed, 20 Jun 2012)

EndedAt: 2012-06-20 23:21:38 -0700 (Wed, 20 Jun 2012)

EllapsedTime: 148.9 seconds

RetCode: 0

Status:  OK

CheckDir: DEXSeq.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/DEXSeq.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 'DEXSeq/DESCRIPTION' ... OK
* this is package 'DEXSeq' version '1.3.2'
* 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 'DEXSeq' 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... 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 'DEXSeq' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'DEXSeq.Rnw' 
** testing if installed package can be loaded

* DONE (DEXSeq)

name	user	system	elapsed
DEUresultTable	0	0	0
DEXSeqHTML	0.000	0.001	0.001
ExonCountSet-class	0	0	0
countTableForGene	0.229	0.013	0.258
counts	0.031	0.003	0.034
design	0.037	0.003	0.039
estimateDispersions	0.000	0.001	0.000
estimateExonDispersionsForModelFrame	0.328	0.036	0.370
estimateSizeFactors	0.062	0.004	0.066
estimatelog2FoldChanges	0	0	0
exonIDs	0.034	0.007	0.042
fitDispersionFunction	14.100	1.666	16.316
geneCountTable	0.068	0.004	0.078
geneIDs	0.041	0.004	0.054
makeCompleteDEUAnalysis	22.726	2.576	26.960
modelFrameForGene	0.045	0.005	0.053
newExonCountSet	0.415	0.036	0.472
plotDEXSeq	0.001	0.000	0.001
read.HTSeqCounts	0.005	0.003	0.009
sizeFactors	0.064	0.005	0.069
subsetByGenes	0.084	0.011	0.097
testForDEU	0	0	0
testGeneForDEU	14.077	1.621	16.150