Package: affycoretools

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes --timings affycoretools_1.20.0.tar.gz

StartedAt: 2010-10-04 15:39:06 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 15:42:30 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 203.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: affycoretools.Rcheck

Warnings: 1

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/affycoretools.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'affycoretools/DESCRIPTION' ... OK
* this is package 'affycoretools' version '1.20.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'affycoretools' can be installed ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... WARNING
Undocumented code objects:
  cv filterfun genefilter kOverA pOverA
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  /Users/biocbuild/bbs-2.6-bioc/meat/affycoretools.Rcheck/00check.log
for details

* install options are ' --no-html'

* installing *source* package ‘affycoretools’ ...
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: AnnotationDbi
Loading required package: DBI
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (affycoretools)

name	user	system	elapsed
annBM	0.001	0.000	0.000
plotDeg	11.816	0.421	12.623
plotPCA	0.070	0.007	0.101
vennCounts2	0.089	0.006	0.102