[R-SIG-Mac] Too many dependencies with BioConductor packages?

[David Winsemius]

On Jun 23, 2009, at 9:29 AM, Gad Abraham wrote:

> On 23/6/09 11:12 PM, Simon Urbanek wrote:
>>>>
>>> Does "install dependencies" only install Depends or also Suggests?
>>>
>>
>> It's equivalent to install.packages(dependencies=TRUE)
>>
>
> OK, so it installs all the Depends, Imports, Suggests, and Enhances.

But does the non-checked Package Installer action mimic what the  
default "dependencies=NA" does?

"The default, NA, means c("Depends", "Imports") if lib is unambiguous,  
and FALSE otherwise."

(I think that means FALSE in my case, since I do not have an  
unambiguous .libPaths(), but for most people it appears to mean NA. )
>
> Maybe this should be mentioned somehow in the GUI (rename "install  
> dependencies"?). It's not too much of an issue for CRAN, but in  
> BioConductor there are large packages (10s of MB at least) which can  
> get downloaded needlessly but are only Suggested.
>
>
As another user I vote "opposed" to that suggestion. I would want the  
Install dependencies check box to do what the naive-user like myself  
would expect, which is to mimic the action of install.packages(<pkg>,  
<url>, dependencies=TRUE).

As an alternative suggestion, it might be helpful to have the R  
command echoed to the GUI console so that a syntactically correct  
template could be modified.

David Winsemius, MD
Heritage Laboratories
West Hartford, CT