Package: ArrayTools

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ArrayTools_1.14.0.tar.gz

StartedAt: 2012-03-23 23:27:44 -0700 (Fri, 23 Mar 2012)

EndedAt: 2012-03-23 23:29:32 -0700 (Fri, 23 Mar 2012)

EllapsedTime: 108.5 seconds

RetCode: 0

Status:  OK

CheckDir: ArrayTools.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/ArrayTools.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 'ArrayTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ArrayTools' version '1.14.0'
* 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 whether package 'ArrayTools' 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
preProcessGeneST: no visible binding for global variable
  'hugene10stCONTROL'
preProcessGeneST: no visible binding for global variable
  'mogene10stCONTROL'
regress: no visible global function definition for 'permute.1'
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking examples ... OK
* 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 'ArrayTools' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'summary' from package 'base' in package 'ArrayTools'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'ArrayTools.Rnw' 
** testing if installed package can be loaded

* DONE (ArrayTools)

name	user	system	elapsed
Output2HTML	0.297	0.021	0.319
QC	0.002	0.000	0.003
Sort	0.141	0.007	0.153
contrastMatrix-class	0.063	0.003	0.066
createExpressionSet	0.154	0.004	0.159
createGSEAFiles	0.011	0.001	0.012
createIndex	0.634	0.024	0.660
createIngenuityFile	0.124	0.005	0.131
designMatrix-class	0.027	0.002	0.029
eSetExample	0.013	0.002	0.014
exprsExample	0.008	0.001	0.009
geneFilter	4.159	0.102	4.301
interactionResult-class	0.536	0.020	0.558
pDataExample	0.002	0.001	0.003
postInteraction	0.376	0.015	0.401
preProcess3prime	6.901	0.244	7.212
preProcessGeneST	0.026	0.003	0.030
qa3prime	0.000	0.000	0.001
qaGeneST	0.026	0.004	0.030
regress	0.132	0.006	0.138
regressResult-class	0.128	0.005	0.135
selectSigGene	0.140	0.011	0.151
selectSigGeneInt	0.381	0.015	0.401