BioC 2.12: CHECK report for DEXSeq on pelham

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: 2013-05-01 04:34:51 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 04:40:44 -0700 (Wed, 01 May 2013)

EllapsedTime: 352.7 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 Patched (2013-04-08 r62531)
* 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 ... [20s/21s] 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 ... [145s/147s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
read.HTSeqCounts        44.515  1.242  46.281
estimateDispersionsTRT  23.930  0.147  24.403
makeCompleteDEUAnalysis 21.444  0.249  21.976
estimateDispersions     14.616  0.295  15.127
testGeneForDEU          12.230  0.632  12.985
fitDispersionFunction   12.737  0.124  13.022
* 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	0.318	0.005	0.323
DEXSeqHTML	0.009	0.003	0.011
ExonCountSet-class	0.010	0.003	0.012
buildExonCountSet	0.010	0.003	0.013
countReadsForDEXSeq	0.012	0.004	0.017
countTableForGene	0.152	0.016	0.183
counts	0.027	0.003	0.031
design	0.034	0.005	0.039
estimateDispersions	14.616	0.295	15.127
estimateDispersionsTRT	23.930	0.147	24.403
estimateExonDispersionsForModelFrame	0.291	0.008	0.305
estimateSizeFactors	0.059	0.005	0.066
estimatelog2FoldChanges	0.012	0.005	0.017
exonIDs	0.030	0.011	0.042
fitDispersionFunction	12.737	0.124	13.022
geneCountTable	0.146	0.004	0.149
geneIDs	0.045	0.004	0.049
makeCompleteDEUAnalysis	21.444	0.249	21.976
modelFrameForGene	0.046	0.008	0.054
modelFrameForTRT	0.036	0.005	0.044
newExonCountSet	0.364	0.010	0.375
perGeneQValue	0.001	0.002	0.004
plotDEXSeq	0.008	0.004	0.012
prepareAnnotationForDEXSeq	0.009	0.004	0.013
read.HTSeqCounts	44.515	1.242	46.281
sizeFactors	0.052	0.007	0.064
subsetByGenes	0.058	0.008	0.066
testForDEU	0.003	0.008	0.011
testForDEUTRT	0.012	0.013	0.024
testGeneForDEU	12.230	0.632	12.985

Summary

Command output