Package: a4Base

Version: 1.2.3

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch a4Base_1.2.3.tar.gz

StartedAt: 2012-03-23 22:51:40 -0700 (Fri, 23 Mar 2012)

EndedAt: 2012-03-23 22:58:27 -0700 (Fri, 23 Mar 2012)

EllapsedTime: 406.8 seconds

RetCode: 0

Status:  OK

CheckDir: a4Base.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/a4Base.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'a4Base/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'a4Base' version '1.2.3'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  'gridSVG' 'JavaGD'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'a4Base' 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 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 ... 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 ... OK
* checking PDF version of manual ... OK

* 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	0.021	0.001	0.023
addQuantilesColors	5.011	0.356	5.741
boxPlot	5.756	0.342	6.614
combineTwoExpressionSet	0	0	0
computeLogRatio	17.363	0.648	18.740
createExpressionSet	0.099	0.001	0.102
filterVarInt	5.096	0.282	5.689
heatmap.expressionSet	0.001	0.002	0.002
histPvalue	5.647	0.338	6.076
histpvalueplotter	5.589	0.352	6.031
lassoReg	5.106	0.311	5.481
logReg	0.000	0.000	0.001
nlcvTT	0	0	0
plot1gene	4.937	0.295	5.337
plotComb2Samples	5.199	0.321	5.633
plotCombMultSamples	5.412	0.416	6.145
plotCombination2genes	5.081	0.299	5.429
plotLogRatio	16.730	0.622	17.774
probabilitiesPlot	0.000	0.001	0.000
probe2gene	5.410	0.202	5.697
profilesPlot	4.858	0.301	5.259
propdegenescalculation	5.623	0.373	6.208
replicates	0.004	0.001	0.003
spectralMap	32.749	5.779	39.432
tTest	5.551	0.449	6.446
volcanoPlot	5.774	0.461	6.412