Package: DEXSeq

Version: 1.4.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings DEXSeq_1.4.0.tar.gz

StartedAt: 2013-03-25 00:40:49 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:43:23 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 154.2 seconds

RetCode: 0

Status:  OK

CheckDir: DEXSeq.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/DEXSeq.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.4.0’
* 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 whether package ‘DEXSeq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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        36.222  0.148  36.591
makeCompleteDEUAnalysis 16.977  0.024  17.294
estimateDispersions     14.465  0.156  15.402
testGeneForDEU           9.141  0.060   9.340
fitDispersionFunction    8.872  0.016   9.020
* 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	0	0
DEXSeqHTML	0	0	0
ExonCountSet-class	0	0	0
countTableForGene	0.204	0.008	0.229
counts	0.016	0.000	0.042
design	0.020	0.000	0.063
estimateDispersions	14.465	0.156	15.402
estimateExonDispersionsForModelFrame	0.212	0.000	0.227
estimateSizeFactors	0.032	0.000	0.038
estimatelog2FoldChanges	0	0	0
exonIDs	0.012	0.004	0.032
fitDispersionFunction	8.872	0.016	9.020
geneCountTable	0.052	0.004	0.057
geneIDs	0.140	0.000	0.143
makeCompleteDEUAnalysis	16.977	0.024	17.294
modelFrameForGene	0.020	0.004	0.040
newExonCountSet	0.256	0.004	0.282
perGeneQValue	0	0	0
plotDEXSeq	0	0	0
read.HTSeqCounts	36.222	0.148	36.591
sizeFactors	0.036	0.000	0.038
subsetByGenes	0.040	0.004	0.046
testForDEU	0	0	0
testGeneForDEU	9.141	0.060	9.340