Package: AffyCompatible

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AffyCompatible_1.14.0.tar.gz

StartedAt: 2012-03-23 23:01:31 -0700 (Fri, 23 Mar 2012)

EndedAt: 2012-03-23 23:05:26 -0700 (Fri, 23 Mar 2012)

EllapsedTime: 235.8 seconds

RetCode: 0

Status:  OK

CheckDir: AffyCompatible.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/AffyCompatible.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 'AffyCompatible/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AffyCompatible' 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 'AffyCompatible' 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 ... OK
* 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 ... NOTE
S3 methods shown with full name in documentation object 'xmlValue.XMLAttributeValue':
  'xmlValue.XMLAttributeValue'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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 'AffyCompatible' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'MAGEAndARR.Rnw' 
   'NetAffxResource.Rnw' 
** testing if installed package can be loaded

* DONE (AffyCompatible)

name	user	system	elapsed
AffyCompatible-class	0.001	0.000	0.002
NetAffxResource-class	0.633	0.050	3.683
readArr	0.846	0.005	0.856
readMage	2.955	0.014	2.993
readNetAffx	0.000	0.000	0.001
readXml	0.145	0.002	0.148
xclass	0.212	0.010	0.226
zzz-ARRCompatibility-class	0.000	0.000	0.002
zzz-DTTCompatibility-class	0.015	0.018	0.033
zzz-NetAffxCompatibility-class	0.001	0.001	0.002