From ripley at stats.ox.ac.uk  Sun Feb  5 17:01:27 2006
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Sun, 5 Feb 2006 16:01:27 +0000 (GMT)
Subject: [Rd] The install.R and R_PROFILE.R files
In-Reply-To: <m2lkwta751.fsf@ziti.local>
References: <Pine.LNX.4.61.0601311817010.20339@gannet.stats>
	<m2ek2mdgvy.fsf@fhcrc.org>
	<Pine.LNX.4.61.0602020703420.9210@gannet.stats>
	<m2lkwta751.fsf@ziti.local>
Message-ID: <Pine.LNX.4.61.0602051557200.24093@gannet.stats>

I had a bumpy ride with this one.

Ruuid/src/Makefile.win refers to src/include, which is not in a binary 
distribution so cannot be installed from an installed version of R 2.2.1. 
(That's a bug report.)

graph throws an S4 signature error in R-devel.

After fixing those, it works with LazyLoad on Windows but not in Unix 
where there is an error in the INSTALL script which I have now fixed.


On Thu, 2 Feb 2006, Seth Falcon wrote:

> Thanks for the explaination of LazyLoad, that's very helpful.
>
> On  1 Feb 2006, ripley at stats.ox.ac.uk wrote:
>> There is no intention to withdraw SaveImage: yes.  Rather, if
>> lazy-loading is not doing a complete job, we could see if it could
>> be improved.
>
> It seems to me that LazyLoad does something different with respect to
> packages listed in Depends and/or how it interacts with namespaces.
>
> I'm testing using the Bioconductor package graph and find that if I
> change SaveImage to LazyLoad I get the following:
>
>   ** preparing package for lazy loading
>   Error in makeClassRepresentation(Class, properties, superClasses, prototype,  :
>           couldn't find function "getuuid"
>
> Looking at the NAMESPACE for the graph package, it looks like it is
> missing some imports.  I added lines:
>  import(Ruuid)
>  exportClasses(Ruuid)
>
> Aside: am I correct in my reading of the extension manual that if one
> uses S4 classes from another package with a namespace, one
> must import the classes and *also* export them?
>
> Now I see this:
>
>    ** preparing package for lazy loading
>    Error in getClass("Ruuid") : "Ruuid" is not a defined class
>    Error: unable to load R code in package 'graph'
>    Execution halted
>
> But Ruuid _is_ defined and exported in the Ruuid package.
>
> Is there a known difference in how dependencies and imports are
> handled with LazyLoad as opposed to SaveImage?
>
> Thanks,
>
> + seth
>
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595



[Rd] The install.R and R_PROFILE.R files
Prof Brian Ripley