Package: DEXSeq

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DEXSeq_1.4.0.tar.gz

StartedAt: 2013-03-24 23:15:57 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 23:18:39 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 162.0 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 2.15.3 (2013-03-01)
* 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 '1.4.0'
* 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 for left-over 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
Examples with CPU or elapsed time > 5s
                          user system elapsed
read.HTSeqCounts        29.195  1.649  31.362
makeCompleteDEUAnalysis 17.591  2.984  21.881
estimateDispersions     14.744  2.215  17.582
fitDispersionFunction   10.221  1.943  12.687
testGeneForDEU           9.151  1.525  11.025
* 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	0.000	0.000	0.001
countTableForGene	0.247	0.020	0.266
counts	0.016	0.003	0.020
design	0.021	0.004	0.026
estimateDispersions	14.744	2.215	17.582
estimateExonDispersionsForModelFrame	0.229	0.048	0.295
estimateSizeFactors	0.041	0.007	0.049
estimatelog2FoldChanges	0	0	0
exonIDs	0.018	0.006	0.024
fitDispersionFunction	10.221	1.943	12.687
geneCountTable	0.042	0.004	0.047
geneIDs	0.027	0.005	0.031
makeCompleteDEUAnalysis	17.591	2.984	21.881
modelFrameForGene	0.025	0.005	0.032
newExonCountSet	0.256	0.029	0.288
perGeneQValue	0	0	0
plotDEXSeq	0	0	0
read.HTSeqCounts	29.195	1.649	31.362
sizeFactors	0.044	0.004	0.048
subsetByGenes	0.051	0.006	0.057
testForDEU	0	0	0
testGeneForDEU	9.151	1.525	11.025