BioC 2.12: CHECK report for DEXSeq on petty

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: 2013-03-25 02:05:57 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:11:19 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 322.4 seconds

RetCode: 0

Status: OK

CheckDir: DEXSeq.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/DEXSeq.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '1.5.9'
* 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 ... [19s/20s] 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 ... [138s/139s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
read.HTSeqCounts        35.391  1.285  36.849
makeCompleteDEUAnalysis 20.876  2.478  23.554
estimateDispersionsTRT  21.748  0.592  22.398
fitDispersionFunction   14.488  1.643  16.257
estimateDispersions     12.848  1.501  14.456
testGeneForDEU          12.699  1.572  14.371
* 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	0.006	0.006	0.012
DEXSeqHTML	0.007	0.007	0.014
ExonCountSet-class	0.003	0.003	0.006
buildExonCountSet	0.008	0.007	0.014
countReadsForDEXSeq	0.007	0.008	0.018
countTableForGene	0.149	0.020	0.171
counts	0.024	0.008	0.034
design	0.026	0.009	0.035
estimateDispersions	12.848	1.501	14.456
estimateDispersionsTRT	21.748	0.592	22.398
estimateExonDispersionsForModelFrame	0.380	0.052	0.436
estimateSizeFactors	0.075	0.012	0.087
estimatelog2FoldChanges	0.010	0.009	0.020
exonIDs	0.035	0.015	0.050
fitDispersionFunction	14.488	1.643	16.257
geneCountTable	0.119	0.014	0.133
geneIDs	0.061	0.014	0.075
makeCompleteDEUAnalysis	20.876	2.478	23.554
modelFrameForGene	0.048	0.013	0.061
modelFrameForTRT	0.046	0.010	0.057
newExonCountSet	0.373	0.036	0.410
perGeneQValue	0.009	0.005	0.015
plotDEXSeq	0.011	0.010	0.024
prepareAnnotationForDEXSeq	0.008	0.007	0.014
read.HTSeqCounts	35.391	1.285	36.849
sizeFactors	0.052	0.011	0.063
subsetByGenes	0.061	0.011	0.071
testForDEU	0.003	0.006	0.009
testForDEUTRT	0.025	0.008	0.033
testGeneForDEU	12.699	1.572	14.371

Summary

Command output