BioC 2.12: CHECK report for DEXSeq on petty

Package: DEXSeq

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DEXSeq_1.6.0.tar.gz

StartedAt: 2013-10-08 22:10:28 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:17:26 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 418.1 seconds

RetCode: 0

Status:  OK

CheckDir: DEXSeq.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/DEXSeq.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'DEXSeq/DESCRIPTION' ... OK
* this is package 'DEXSeq' version '1.6.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'DEXSeq' can be installed ... [24s/24s] OK
* checking installed package size ... OK
* checking package directory ... 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 ... [173s/178s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
read.HTSeqCounts        51.219  0.965  53.339
estimateDispersionsTRT  29.449  0.089  30.199
makeCompleteDEUAnalysis 27.022  0.133  28.808
estimateDispersions     17.769  0.296  18.219
testGeneForDEU          15.789  0.411  16.401
fitDispersionFunction   15.232  0.075  15.969
* 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
** testing if installed package can be loaded
* DONE (DEXSeq)

name	user	system	elapsed
DEUresultTable	0.293	0.003	0.303
DEXSeqHTML	0.009	0.003	0.011
ExonCountSet-class	0.005	0.001	0.006
buildExonCountSet	0.008	0.002	0.011
countReadsForDEXSeq	0.012	0.003	0.014
countTableForGene	0.202	0.010	0.213
counts	0.032	0.004	0.036
design	0.036	0.003	0.040
estimateDispersions	17.769	0.296	18.219
estimateDispersionsTRT	29.449	0.089	30.199
estimateExonDispersionsForModelFrame	0.395	0.004	0.463
estimateSizeFactors	0.065	0.004	0.074
estimatelog2FoldChanges	0.007	0.002	0.010
exonIDs	0.030	0.007	0.039
fitDispersionFunction	15.232	0.075	15.969
geneCountTable	0.160	0.005	0.172
geneIDs	0.041	0.004	0.050
makeCompleteDEUAnalysis	27.022	0.133	28.808
modelFrameForGene	0.049	0.006	0.055
modelFrameForTRT	0.042	0.005	0.050
newExonCountSet	0.438	0.010	0.462
perGeneQValue	0.007	0.002	0.008
plotDEXSeq	0.007	0.004	0.012
prepareAnnotationForDEXSeq	0.008	0.003	0.011
read.HTSeqCounts	51.219	0.965	53.339
sizeFactors	0.064	0.007	0.087
subsetByGenes	0.087	0.007	0.094
testForDEU	0.003	0.004	0.007
testForDEUTRT	0.044	0.007	0.050
testGeneForDEU	15.789	0.411	16.401