BioC 2.12: CHECK report for DEXSeq on george2

Package: DEXSeq

Version: 1.6.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings DEXSeq_1.6.0.tar.gz

StartedAt: 2013-10-09 01:20:59 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 01:28:10 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 430.6 seconds

RetCode: 0

Status:  OK

CheckDir: DEXSeq.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/DEXSeq.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.6.0’
* 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 ... [24s/24s] 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 ... [180s/184s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
read.HTSeqCounts        62.132  0.300  66.628
makeCompleteDEUAnalysis 26.206  0.020  26.468
estimateDispersionsTRT  25.338  0.020  25.363
estimateDispersions     17.785  0.152  17.939
fitDispersionFunction   16.117  0.080  16.199
testGeneForDEU          14.817  0.040  14.982
* 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	0.540	0.012	0.552
DEXSeqHTML	0.012	0.008	0.020
ExonCountSet-class	0.016	0.004	0.018
buildExonCountSet	0.012	0.016	0.025
countReadsForDEXSeq	0.020	0.008	0.027
countTableForGene	0.156	0.016	0.170
counts	0.532	0.000	0.533
design	0.040	0.004	0.043
estimateDispersions	17.785	0.152	17.939
estimateDispersionsTRT	25.338	0.020	25.363
estimateExonDispersionsForModelFrame	0.368	0.000	0.370
estimateSizeFactors	0.068	0.000	0.069
estimatelog2FoldChanges	0.028	0.000	0.026
exonIDs	0.052	0.004	0.055
fitDispersionFunction	16.117	0.080	16.199
geneCountTable	0.188	0.000	0.190
geneIDs	0.192	0.004	0.198
makeCompleteDEUAnalysis	26.206	0.020	26.468
modelFrameForGene	0.048	0.008	0.056
modelFrameForTRT	0.052	0.004	0.056
newExonCountSet	0.472	0.012	0.485
perGeneQValue	0.012	0.000	0.013
plotDEXSeq	0.024	0.000	0.025
prepareAnnotationForDEXSeq	0.024	0.000	0.025
read.HTSeqCounts	62.132	0.300	66.628
sizeFactors	0.060	0.000	0.063
subsetByGenes	0.156	0.012	0.167
testForDEU	0.008	0.000	0.007
testForDEUTRT	0.004	0.000	0.007
testGeneForDEU	14.817	0.040	14.982