BioC 2.12: CHECK report for DEXSeq on pelham

Package: DEXSeq

Version: 1.5.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DEXSeq_1.5.9.tar.gz

StartedAt: 2013-03-24 04:25:43 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 04:31:46 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 363.6 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 3.0.0 beta (2013-03-21 r62346)
* 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 '1.5.9'
* 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 ... [21s/22s] 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 installed files from 'inst/doc' ... OK
* checking examples ... [155s/156s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
read.HTSeqCounts        47.762  1.299  49.549
estimateDispersionsTRT  24.830  0.122  25.145
makeCompleteDEUAnalysis 23.147  0.178  23.415
estimateDispersions     15.565  0.249  16.094
testGeneForDEU          14.101  0.429  14.595
fitDispersionFunction   14.019  0.106  14.185
* 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	0.008	0.003	0.012
DEXSeqHTML	0.009	0.003	0.013
ExonCountSet-class	0.005	0.001	0.006
buildExonCountSet	0.014	0.004	0.018
countReadsForDEXSeq	0.012	0.004	0.016
countTableForGene	0.164	0.014	0.184
counts	0.335	0.006	0.342
design	0.035	0.005	0.039
estimateDispersions	15.565	0.249	16.094
estimateDispersionsTRT	24.830	0.122	25.145
estimateExonDispersionsForModelFrame	0.372	0.006	0.380
estimateSizeFactors	0.062	0.006	0.068
estimatelog2FoldChanges	0.009	0.003	0.013
exonIDs	0.030	0.011	0.042
fitDispersionFunction	14.019	0.106	14.185
geneCountTable	0.149	0.005	0.159
geneIDs	0.052	0.004	0.055
makeCompleteDEUAnalysis	23.147	0.178	23.415
modelFrameForGene	0.046	0.006	0.052
modelFrameForTRT	0.043	0.005	0.048
newExonCountSet	0.361	0.005	0.366
perGeneQValue	0.009	0.003	0.011
plotDEXSeq	0.017	0.005	0.021
prepareAnnotationForDEXSeq	0.008	0.002	0.011
read.HTSeqCounts	47.762	1.299	49.549
sizeFactors	0.058	0.008	0.066
subsetByGenes	0.072	0.006	0.078
testForDEU	0.044	0.009	0.056
testForDEUTRT	0.003	0.006	0.009
testGeneForDEU	14.101	0.429	14.595

Summary

Command output