Package: ArrayTools

Version: 1.11.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ArrayTools_1.11.0.tar.gz

StartedAt: 2011-03-17 15:34:45 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 15:36:01 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 75.9 seconds

RetCode: 0

Status:  OK

CheckDir: ArrayTools.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/ArrayTools.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* 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 '1.11.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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'
regress: no visible binding for global variable 'design'
* 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 package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'ArrayTools' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Creating a new generic function for "summary" in "ArrayTools"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (ArrayTools)

name	user	system	elapsed
Output2HTML	0.147	0.005	0.152
QC	0.001	0.000	0.002
Sort	0.135	0.001	0.137
contrastMatrix-class	0.054	0.002	0.056
createExpressionSet	0.107	0.001	0.108
createGSEAFiles	0.007	0.001	0.008
createIndex	0.387	0.002	0.389
createIngenuityFile	0.091	0.001	0.092
designMatrix-class	0.021	0.001	0.022
eSetExample	0.007	0.000	0.008
exprsExample	0.005	0.000	0.006
geneFilter	0.883	0.011	0.893
interactionResult-class	0.289	0.005	0.294
pDataExample	0.001	0.001	0.002
postInteraction	0.280	0.001	0.281
preProcess3prime	4.705	0.083	4.788
preProcessGeneST	0.017	0.001	0.018
qa3prime	0	0	0
qaGeneST	0.016	0.001	0.017
regress	0.098	0.006	0.104
regressResult-class	0.120	0.009	0.128
selectSigGene	0.103	0.001	0.104
selectSigGeneInt	0.329	0.001	0.331