BioC 2.13: CHECK report for DEXSeq on zin1

Package: DEXSeq

Version: 1.8.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings DEXSeq_1.8.0.tar.gz

StartedAt: 2014-04-05 00:45:53 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 00:49:54 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 240.8 seconds

RetCode: 0

Status:  OK

CheckDir: DEXSeq.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/DEXSeq.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.8.0’
* 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 ... [12s/12s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
‘:::’ call which should be ‘::’: ‘parallel:::mclapply’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘DEXSeq.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [125s/125s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
doCompleteDEUAnalysis      23.965  0.028  24.128
plotDispEsts-methods       16.249  0.004  16.283
estimateDispersions_BM     15.473  0.000  15.501
fitDispersionFunction      14.933  0.004  14.962
estimateDispersions        14.813  0.012  14.851
read.HTSeqCounts           12.697  0.072  12.815
makeCompleteDEUAnalysis_BM 12.293  0.012  12.324
testGeneForDEU              7.280  0.028   7.318
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/DEXSeq.Rcheck/00check.log’
for details.

* 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	0.164	0.000	0.165
DEXSeqHTML	0.004	0.000	0.004
ExonCountSet-class	0.000	0.000	0.002
buildExonCountSet	0.004	0.000	0.004
constructModelFrame	0.048	0.000	0.049
countReadsForDEXSeq	0.004	0.000	0.005
countTableForGene	0.064	0.012	0.077
counts	0.016	0.000	0.015
design	0.016	0.000	0.016
doCompleteDEUAnalysis	23.965	0.028	24.128
estimateDispersions	14.813	0.012	14.851
estimateDispersions_BM	15.473	0.000	15.501
estimateExonDispersionsForModelFrame_BM	0.184	0.000	0.183
estimateSizeFactors	0.036	0.000	0.035
estimatelog2FoldChanges	0.004	0.000	0.005
exonIDs	0.020	0.000	0.021
fitDispersionFunction	14.933	0.004	14.962
geneCountTable	0.064	0.008	0.071
geneIDs	0.108	0.000	0.106
makeCompleteDEUAnalysis_BM	12.293	0.012	12.324
modelFrameForGene	0.024	0.000	0.025
newExonCountSet	0.184	0.000	0.185
perGeneQValue	0.004	0.000	0.003
plotDEXSeq	0.004	0.000	0.005
plotDispEsts-methods	16.249	0.004	16.283
plotMA-methods	0.004	0.000	0.004
prepareAnnotationForDEXSeq-deprecated	0.000	0.004	0.005
read.HTSeqCounts	12.697	0.072	12.815
sizeFactors	0.032	0.000	0.032
subsetByGenes	0.096	0.000	0.096
testForDEU	0.000	0.000	0.001
testForDEU_BM	0.016	0.000	0.013
testGeneForDEU	7.280	0.028	7.318