Package: a4Base

Version: 1.2.3

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings a4Base_1.2.3.tar.gz

StartedAt: 2012-03-23 22:47:43 -0700 (Fri, 23 Mar 2012)

EndedAt: 2012-03-23 22:53:02 -0700 (Fri, 23 Mar 2012)

EllapsedTime: 318.8 seconds

RetCode: 0

Status:  OK

CheckDir: a4Base.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/a4Base.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.2.3’
* 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	0.012	0.000	0.013
addQuantilesColors	4.036	0.160	4.195
boxPlot	3.589	0.108	3.710
combineTwoExpressionSet	0.004	0.000	0.001
computeLogRatio	17.129	0.336	18.866
createExpressionSet	0.064	0.000	0.069
filterVarInt	3.100	0.108	3.378
heatmap.expressionSet	0.004	0.000	0.003
histPvalue	3.604	0.072	3.752
histpvalueplotter	3.648	0.100	3.879
lassoReg	3.517	0.088	4.028
logReg	0	0	0
nlcvTT	0.000	0.000	0.001
plot1gene	3.688	0.180	4.166
plotComb2Samples	3.872	0.156	4.292
plotCombMultSamples	5.124	0.052	5.209
plotCombination2genes	3.124	0.068	3.227
plotLogRatio	15.661	0.224	16.596
probabilitiesPlot	0	0	0
probe2gene	3.353	0.052	3.468
profilesPlot	2.672	0.036	2.742
propdegenescalculation	3.408	0.040	3.454
replicates	0.004	0.000	0.004
spectralMap	33.678	0.444	34.810
tTest	4.076	0.068	4.173
volcanoPlot	4.105	0.072	4.314