Package: ArrayTools

Version: 1.11.0

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings ArrayTools_1.11.0.tar.gz

StartedAt: 2011-02-24 17:44:49 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 17:45:41 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 52.6 seconds

RetCode: 0

Status:  OK

CheckDir: ArrayTools.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/ArrayTools.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 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 data for non-ASCII characters ... 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	0.204	0.000	0.202
QC	0.000	0.000	0.002
Sort	0.168	0.000	0.169
contrastMatrix-class	0.052	0.000	0.049
createExpressionSet	0.096	0.000	0.101
createGSEAFiles	0.008	0.000	0.007
createIndex	0.436	0.016	0.451
createIngenuityFile	0.092	0.004	0.093
designMatrix-class	0.020	0.000	0.019
eSetExample	0.004	0.000	0.005
exprsExample	0.004	0.000	0.004
geneFilter	0.844	0.032	0.899
interactionResult-class	0.380	0.004	0.385
pDataExample	0.000	0.000	0.002
postInteraction	0.352	0.016	0.366
preProcess3prime	5.268	0.072	6.798
preProcessGeneST	0.008	0.008	0.015
qa3prime	0	0	0
qaGeneST	0.016	0.000	0.014
regress	0.088	0.008	0.098
regressResult-class	0.108	0.004	0.110
selectSigGene	0.116	0.000	0.115
selectSigGeneInt	0.32	0.00	0.32