Interesting, I can't replicate this.  Perhaps it has to do with package versions
(of other attached packages?):
> sessionInfo()
Version 2.3.0 (2006-04-24)
x86_64-unknown-linux-gnu
 
attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "base"
 
other attached packages:
ontoElicitor      Biobase         RBGL        graph        Ruuid
     "0.0.4"     "1.11.0"      "1.6.0"     "1.11.0"      "1.9.2"

sfalcon@gopher6:~/proj/SGDI/Software/Rpacks> R CMD build ontoElicitor
* checking for file 'ontoElicitor/DESCRIPTION' ... OK
* preparing 'ontoElicitor':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* Installing *source* package 'ontoElicitor' ...
** R
** data
** inst
** help
 >>> Building/Updating help pages for package 'ontoElicitor'
     Formats: text html latex example 
  breastOnto                        text    html    latex   example
     missing link(s):  buildOntoHTML
** building package indices ...
* DONE (ontoElicitor)
* creating vignettes ... ERROR

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.


Error:  chunk 1 (label=buildOnto) 
Error in buildOntoHTML(breastOnto, "SGDI Breast Cancer", tDir) : 
        subscript out of bounds
Error in buildVignettes(dir = ".") : Error:  chunk 1 (label=buildOnto) 
Error in buildOntoHTML(breastOnto, "SGDI Breast Cancer", tDir) : 
        subscript out of bounds
Execution halted