Package: DEXSeq

Version: 1.0.2

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings DEXSeq_1.0.2.tar.gz

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

EndedAt: 2012-03-24 00:05:06 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 76.9 seconds

RetCode: 0

Status:  OK

CheckDir: DEXSeq.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/DEXSeq.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEXSeq/DESCRIPTION’ ... OK
* this is package ‘DEXSeq’ version ‘1.0.2’
* 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 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 ...
*** tangling vignette sources ...
   ‘DEXSeq.Rnw’ 
** testing if installed package can be loaded

* DONE (DEXSeq)

name	user	system	elapsed
DEUresultTable	0.000	0.000	0.001
DEXSeqHTML	0	0	0
ExonCountSet-class	0	0	0
countTableForGene	0.272	0.004	0.275
counts	0.02	0.00	0.02
design	0.012	0.008	0.025
estimateDispersions	0.000	0.000	0.001
estimateExonDispersionsForModelFrame	0.284	0.008	0.292
estimateSizeFactors	0.040	0.000	0.042
estimatelog2FoldChanges	0	0	0
exonIDs	0.024	0.004	0.024
fitDispersionFunction	9.664	0.024	9.771
geneCountTable	0.072	0.004	0.079
geneIDs	0.144	0.000	0.155
makeCompleteDEUAnalysis	17.309	0.012	17.845
modelFrameForGene	0.020	0.008	0.031
newExonCountSet	0.34	0.00	0.34
plotDEXSeq	0	0	0
read.HTSeqCounts	0.008	0.000	0.007
sizeFactors	0.032	0.008	0.041
subsetByGenes	0.048	0.000	0.049
testForDEU	0	0	0
testGeneForDEU	10.021	0.000	10.025