Package: DEXSeq

Version: 1.2.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings DEXSeq_1.2.0.tar.gz

StartedAt: 2012-04-01 00:36:10 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 00:37:23 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 72.5 seconds

RetCode: 0

Status:  OK

CheckDir: DEXSeq.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/DEXSeq.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DEXSeq/DESCRIPTION' ... OK
* this is package 'DEXSeq' version '1.2.0'
* 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 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	0	0
ExonCountSet-class	0	0	0
countTableForGene	0.140	0.004	0.146
counts	0.012	0.004	0.021
design	0.020	0.004	0.033
estimateDispersions	0.000	0.000	0.001
estimateExonDispersionsForModelFrame	0.248	0.000	0.252
estimateSizeFactors	0.028	0.008	0.041
estimatelog2FoldChanges	0.000	0.000	0.001
exonIDs	0.024	0.000	0.035
fitDispersionFunction	7.120	0.012	7.140
geneCountTable	0.028	0.004	0.037
geneIDs	0.024	0.000	0.028
makeCompleteDEUAnalysis	12.441	0.012	12.463
modelFrameForGene	0.020	0.004	0.028
newExonCountSet	0.240	0.000	0.244
plotDEXSeq	0	0	0
read.HTSeqCounts	0.004	0.000	0.013
sizeFactors	0.032	0.004	0.039
subsetByGenes	0.036	0.004	0.041
testForDEU	0	0	0
testGeneForDEU	6.920	0.008	6.936