Package: ArrayTools

Version: 1.12.0

Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch ArrayTools_1.12.0.tar.gz

StartedAt: 2011-10-20 13:05:47 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 13:07:05 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 78.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ArrayTools.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/ArrayTools.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ArrayTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ArrayTools' version '1.12.0'
* checking package namespace 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 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'
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 for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... WARNING
Package vignette(s) without corresponding PDF:
   ArrayTools.Rnw

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.8-bioc/meat/ArrayTools.Rcheck/00check.log'
for details

* installing *source* package 'ArrayTools' ...
** R
** data
** inst
** preparing package for lazy loading
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	0.22	0.00	0.22
QC	0	0	0
Sort	0.11	0.00	0.11
contrastMatrix-class	0.06	0.00	0.06
createExpressionSet	0.11	0.00	0.11
createGSEAFiles	0	0	0
createIndex	0.49	0.00	0.48
createIngenuityFile	0.17	0.00	0.18
designMatrix-class	0.01	0.00	0.01
eSetExample	0.02	0.00	0.02
exprsExample	0	0	0
geneFilter	0.72	0.00	0.72
interactionResult-class	0.37	0.00	0.37
pDataExample	0.02	0.00	0.02
postInteraction	0.29	0.00	0.29
preProcess3prime	5.35	0.11	5.49
preProcessGeneST	0.02	0.00	0.02
qa3prime	0	0	0
qaGeneST	0.02	0.00	0.01
regress	0.31	0.01	0.33
regressResult-class	0.11	0.00	0.11
selectSigGene	0.11	0.00	0.11
selectSigGeneInt	0.32	0.00	0.33