BioC 2.13: CHECK report for DEXSeq on perceval

Package: DEXSeq

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DEXSeq_1.8.0.tar.gz

StartedAt: 2014-04-05 00:48:28 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 00:57:47 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 558.9 seconds

RetCode: 0

Status:  OK

CheckDir: DEXSeq.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/DEXSeq.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEXSeq/DESCRIPTION’ ... OK
* this is package ‘DEXSeq’ version ‘1.8.0’
* 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 ... [19s/57s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
‘:::’ call which should be ‘::’: ‘parallel:::mclapply’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘DEXSeq.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [252s/253s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
doCompleteDEUAnalysis      54.213  0.170  54.735
plotDispEsts-methods       32.667  0.095  33.462
fitDispersionFunction      32.073  0.069  32.318
estimateDispersions        31.088  0.081  31.372
estimateDispersions_BM     30.828  0.078  30.996
read.HTSeqCounts           27.986  0.981  29.006
makeCompleteDEUAnalysis_BM 19.194  0.164  19.368
testGeneForDEU              9.956  0.215  10.202
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/DEXSeq.Rcheck/00check.log’
for details.

* 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	0.376	0.003	0.379
DEXSeqHTML	0.005	0.002	0.007
ExonCountSet-class	0.005	0.001	0.006
buildExonCountSet	0.008	0.002	0.010
constructModelFrame	0.075	0.005	0.080
countReadsForDEXSeq	0.009	0.003	0.012
countTableForGene	0.120	0.008	0.129
counts	0.024	0.002	0.027
design	0.033	0.003	0.035
doCompleteDEUAnalysis	54.213	0.170	54.735
estimateDispersions	31.088	0.081	31.372
estimateDispersions_BM	30.828	0.078	30.996
estimateExonDispersionsForModelFrame_BM	0.242	0.004	0.246
estimateSizeFactors	0.056	0.002	0.058
estimatelog2FoldChanges	0.010	0.003	0.012
exonIDs	0.035	0.008	0.043
fitDispersionFunction	32.073	0.069	32.318
geneCountTable	0.112	0.003	0.116
geneIDs	0.244	0.003	0.248
makeCompleteDEUAnalysis_BM	19.194	0.164	19.368
modelFrameForGene	0.047	0.006	0.052
newExonCountSet	0.329	0.004	0.333
perGeneQValue	0.009	0.001	0.011
plotDEXSeq	0.010	0.002	0.012
plotDispEsts-methods	32.667	0.095	33.462
plotMA-methods	0.010	0.002	0.012
prepareAnnotationForDEXSeq-deprecated	0.009	0.002	0.011
read.HTSeqCounts	27.986	0.981	29.006
sizeFactors	0.045	0.006	0.051
subsetByGenes	0.101	0.007	0.108
testForDEU	0.026	0.013	0.040
testForDEU_BM	0.003	0.005	0.007
testGeneForDEU	9.956	0.215	10.202