BioC 2.12: CHECK report for DEXSeq on george2

Package: DEXSeq

Version: 1.5.9

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings DEXSeq_1.5.9.tar.gz

StartedAt: 2013-03-25 01:10:44 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:17:58 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 434.5 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 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.5.9’
* 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 ... [26s/28s] 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 ... [178s/187s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
read.HTSeqCounts        59.075  0.248  60.164
makeCompleteDEUAnalysis 26.650  0.016  28.752
estimateDispersionsTRT  24.486  0.052  26.624
estimateDispersions     17.933  0.168  18.544
testGeneForDEU          16.974  0.048  17.085
fitDispersionFunction   15.381  0.036  18.874
* 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	0.012	0.016	0.028
DEXSeqHTML	0.012	0.004	0.018
ExonCountSet-class	0.004	0.008	0.012
buildExonCountSet	0.016	0.008	0.023
countReadsForDEXSeq	0.012	0.008	0.018
countTableForGene	0.172	0.020	0.193
counts	0.616	0.008	0.714
design	0.040	0.000	0.041
estimateDispersions	17.933	0.168	18.544
estimateDispersionsTRT	24.486	0.052	26.624
estimateExonDispersionsForModelFrame	0.340	0.000	0.341
estimateSizeFactors	0.060	0.000	0.058
estimatelog2FoldChanges	0.012	0.004	0.016
exonIDs	0.044	0.004	0.049
fitDispersionFunction	15.381	0.036	18.874
geneCountTable	0.276	0.000	0.278
geneIDs	0.184	0.004	0.234
makeCompleteDEUAnalysis	26.650	0.016	28.752
modelFrameForGene	0.048	0.008	0.057
modelFrameForTRT	0.056	0.012	0.070
newExonCountSet	0.496	0.000	0.496
perGeneQValue	0.004	0.000	0.006
plotDEXSeq	0.032	0.000	0.032
prepareAnnotationForDEXSeq	0.024	0.000	0.023
read.HTSeqCounts	59.075	0.248	60.164
sizeFactors	0.064	0.000	0.065
subsetByGenes	0.088	0.000	0.091
testForDEU	0.008	0.000	0.009
testForDEUTRT	0.072	0.000	0.074
testGeneForDEU	16.974	0.048	17.085

Summary

Command output