BioC 2.13: CHECK report for a4Base on perceval

Package: a4Base

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch a4Base_1.10.0.tar.gz

StartedAt: 2014-04-04 23:07:34 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 23:14:33 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 419.0 seconds

RetCode: 0

Status:  OK

CheckDir: a4Base.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/a4Base.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘a4Base/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘a4Base’ version ‘1.10.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘JavaGD’
* 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 ‘a4Base’ can be installed ... [30s/31s] 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 dependencies in R code ... NOTE
‘library’ or ‘require’ calls to packages already attached by Depends:
  ‘Biobase’ ‘grid’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘a4Preproc’ ‘annaffy’ ‘AnnotationDbi’ ‘genefilter’ ‘glmnet’ ‘gplots’
  ‘mpm’ ‘multtest’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 ... NOTE
plotLogRatio: no visible global function definition for ‘JavaGD’
plotLogRatio: no visible global function definition for ‘grid.garnish’
plotLogRatio: no visible global function definition for
  ‘grid.hyperlink’
plotLogRatio: no visible global function definition for ‘grid.script’
plotLogRatio: no visible global function definition for ‘gridToSVG’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [137s/156s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
spectralMap            32.679  1.665  39.760
computeLogRatio        16.299  0.420  17.384
plotLogRatio           14.250  0.363  18.141
boxPlot                 5.188  0.262   5.533
addQuantilesColors      4.873  0.259   5.157
probe2gene              3.568  0.203   6.661
propdegenescalculation  3.396  0.179   5.110
profilesPlot            2.974  0.162   5.156
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/a4Base.Rcheck/00check.log’
for details.

* installing *source* package ‘a4Base’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (a4Base)

name	user	system	elapsed
a4palette	0.474	0.004	0.478
addQuantilesColors	4.873	0.259	5.157
boxPlot	5.188	0.262	5.533
combineTwoExpressionSet	0.004	0.006	0.010
computeLogRatio	16.299	0.420	17.384
createExpressionSet	0.092	0.017	0.109
filterVarInt	2.961	0.192	3.232
heatmap.expressionSet	0.063	0.066	0.129
histPvalue	3.729	0.214	4.228
histpvalueplotter	3.721	0.187	4.013
lassoReg	3.070	0.168	3.326
logReg	0.032	0.008	0.040
nlcvTT	0.002	0.005	0.008
plot1gene	3.330	0.168	3.592
plotComb2Samples	3.546	0.211	3.941
plotCombMultSamples	3.582	0.234	4.851
plotCombination2genes	3.137	0.163	3.331
plotLogRatio	14.250	0.363	18.141
probabilitiesPlot	0.022	0.015	0.038
probe2gene	3.568	0.203	6.661
profilesPlot	2.974	0.162	5.156
propdegenescalculation	3.396	0.179	5.110
replicates	0.006	0.005	0.019
spectralMap	32.679	1.665	39.760
tTest	3.699	0.254	4.425
volcanoPlot	3.212	0.200	3.650