Package: AffyCompatible

Version: 1.19.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AffyCompatible_1.19.2.tar.gz

StartedAt: 2013-03-24 01:57:37 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 02:02:12 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 274.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: AffyCompatible.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/AffyCompatible.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'AffyCompatible/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AffyCompatible' version '1.19.2'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'AffyCompatible' can be installed ... [55s/57s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 ... WARNING
xmlValue:
  function(x, ignoreComments, recursive, encoding, trim)
xmlValue.XMLAttributeValue:
  function(x, ignoreComments, recursive, encoding)

xmlValue:
  function(x, ignoreComments, recursive, encoding, trim)
xmlValue.XMLAttributeValue:
  function(x, ignoreComments, recursive, encoding)

See section 'Generic functions and methods' of the 'Writing R
Extensions' manual.
* 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [30s/38s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
NetAffxResource-class 14.857  0.385  22.629
* 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

WARNING: There was 1 warning.
See
  '/Users/biocbuild/bbs-2.12-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	0.010	0.004	0.014
NetAffxResource-class	14.857	0.385	22.629
readArr	1.109	0.091	1.226
readMage	2.743	0.020	2.782
readNetAffx	0.003	0.005	0.008
readXml	0.153	0.011	0.169
xclass	0.214	0.016	0.233
zzz-ARRCompatibility-class	0.017	0.024	0.042
zzz-DTTCompatibility-class	0.486	0.539	1.040
zzz-NetAffxCompatibility-class	0.017	0.018	0.036