Package: AffyCompatible

Version: 1.17.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AffyCompatible_1.17.0.tar.gz

StartedAt: 2012-06-20 21:27:42 -0700 (Wed, 20 Jun 2012)

EndedAt: 2012-06-20 21:31:54 -0700 (Wed, 20 Jun 2012)

EllapsedTime: 252.7 seconds

RetCode: 0

Status:  OK

CheckDir: AffyCompatible.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/AffyCompatible.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* 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 '1.17.0'
* 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 ... NOTE
.readXmlAsClass: warning in xmlTreeParse(fl, useInternal = TRUE, ...):
  partial argument match of 'useInternal' to 'useInternalNodes'
readXml: warning in xmlTreeParse(fl, useInternal = TRUE, ...): partial
  argument match of 'useInternal' to 'useInternalNodes'
* 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 installed files from '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

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/AffyCompatible.Rcheck/00check.log'
for details.

* installing *source* package 'AffyCompatible' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   '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	0.796	0.079	5.969
readArr	0.746	0.007	0.777
readMage	3.007	0.009	3.042
readNetAffx	0.001	0.000	0.000
readXml	0.151	0.003	0.154
xclass	0.233	0.010	0.244
zzz-ARRCompatibility-class	0.000	0.000	0.001
zzz-DTTCompatibility-class	0.014	0.017	0.032
zzz-NetAffxCompatibility-class	0.001	0.001	0.002