Package: affycoretools

Version: 1.26.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch affycoretools_1.26.0.tar.gz

StartedAt: 2012-01-09 00:56:20 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 00:59:37 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 197.2 seconds

RetCode: 0

Status:  OK

CheckDir: affycoretools.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/affycoretools.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affycoretools/DESCRIPTION' ... OK
* this is package 'affycoretools' version '1.26.0'
* 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 'affycoretools' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
* 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
File 'affycoretools/R/zzz.R':
  .onLoad calls:
    require(Biobase)

Package startup functions should not change the search path.
See section 'Good practice' in ?.onAttach.

* 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 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 'affycoretools' ...
** R
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "connection" in package 'graph' seems equivalent to one from package 'IRanges' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "file" in package 'graph' seems equivalent to one from package 'IRanges' and is not turning on duplicate class definitions for this class
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'affycoretools.Rnw' 
   'affycoretools_biomaRt.Rnw' 
** testing if installed package can be loaded

* DONE (affycoretools)

name	user	system	elapsed
annBM	0	0	0
plotDeg	12.53	0.11	12.66
plotPCA	0.06	0.00	0.23
vennCounts2	0.05	0.00	0.05