BioC 2.12: CHECK report for DEXSeq on lamb2

Package: DEXSeq

Version: 1.5.6

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings DEXSeq_1.5.6.tar.gz

StartedAt: 2013-01-16 02:03:46 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 02:06:40 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 173.7 seconds

RetCode: 0

Status: OK

CheckDir: DEXSeq.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/DEXSeq.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEXSeq/DESCRIPTION’ ... OK
* this is package ‘DEXSeq’ version ‘1.5.6’
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
read.HTSeqCounts        36.374  0.164  36.606
estimateDispersionsTRT  18.117  0.020  18.140
makeCompleteDEUAnalysis 17.537  0.000  17.543
estimateDispersions     14.721  0.116  14.844
testGeneForDEU          10.524  0.004  10.528
fitDispersionFunction   10.108  0.012  10.122
* 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	0.020	0.000	0.019
DEXSeqHTML	0.012	0.000	0.014
ExonCountSet-class	0.004	0.000	0.005
countTableForGene	0.256	0.000	0.271
counts	0.024	0.004	0.025
design	0.028	0.000	0.027
estimateDispersions	14.721	0.116	14.844
estimateDispersionsTRT	18.117	0.020	18.140
estimateExonDispersionsForModelFrame	0.236	0.000	0.236
estimateSizeFactors	0.040	0.004	0.044
estimatelog2FoldChanges	0.016	0.000	0.013
exonIDs	0.032	0.004	0.034
fitDispersionFunction	10.108	0.012	10.122
geneCountTable	0.056	0.004	0.059
geneIDs	0.128	0.004	0.133
makeCompleteDEUAnalysis	17.537	0.000	17.543
modelFrameForGene	0.064	0.000	0.061
modelFrameForTRT	0.052	0.004	0.056
newExonCountSet	0.785	0.004	0.786
perGeneQValue	0.016	0.000	0.014
plotDEXSeq	0.028	0.000	0.030
read.HTSeqCounts	36.374	0.164	36.606
sizeFactors	0.076	0.000	0.079
subsetByGenes	0.052	0.000	0.053
testForDEU	0.008	0.000	0.006
testForDEUTRT	0.004	0.000	0.004
testGeneForDEU	10.524	0.004	10.528

Summary

Command output