Package: farms

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch farms_1.6.0.tar.gz

StartedAt: 2012-03-24 00:53:40 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 00:54:43 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 62.9 seconds

RetCode: 0

Status:  OK

CheckDir: farms.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/farms.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 'farms/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'farms' version '1.6.0'
* 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 'farms' 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
File 'farms/R/zzz.R':
  .onLoad calls:
    require("methods", quietly = TRUE)
    require(utils)
    require(Biobase, quietly = TRUE)
    require(affy, quietly = TRUE)

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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 'farms' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'farms.Rnw' 
** testing if installed package can be loaded

* DONE (farms)

name	user	system	elapsed
INI_Calls-class	0.300	0.012	0.313
INIcalls-methods	0.916	0.046	0.986
expFarms	0.066	0.001	0.068
generateExprVal.method.farms	0.011	0.001	0.040
getI_Eset-methods	0.933	0.045	1.056
getI_ProbeSets-methods	0.906	0.041	0.950
getNI_Eset-methods	0.917	0.043	0.965
getNI_ProbeSets-methods	0.922	0.044	0.974
lFarms	0.148	0.007	0.156
plot-methods	0.910	0.045	0.967
qFarms	0.062	0.002	0.063
summary-methods	0.903	0.039	0.960