Dear Laurent,

Thanks for the suggestions. As a short-term solution, I will use the 
extra slots in the 'CdfEnvAff' class and save that as an R object.

As a long-term solution (rather than hacking the 'makecdfenv' package), 
we may want to kindly ask Wolfgang or Rafael to add this functionality 
to their package...

Best,
Norman

Norman Pavelka
Department of Biotechnology and Bioscience
University of Milano-Bicocca
Piazza della Scienza, 2
20126 Milan, Italy

Phone: +39 02 6448 3556
Fax: +39 02 6448 3552

On 26 Nov 2005, at 08:13, lgautier@altern.org wrote:

>> Meanwhile, I have a new question for Laurent (or any other BioC
>> contributor): "How can I make a CDF package from my brand new
>> alternative CDF environment?"
>
> You may have to write your own code to do so (see second comment 
> below).
> However, you can also save your R object in a file
> (command "save"), then load it and have the few
> lines on page 5 of the vignette
> http://www.bioconductor.org/repository/devel/vignette/altcdfenvs.pdf
> whenever needed.
>
>> I saw in the vignette of package 'makecdfenv' how to make a CDF
>> environment or a CDF package starting from an Affy-provided CDF file,
>> but not how to convert an already existing CDF environment into a CDF
>> package... This would make it more easy for me to share it and also to
>> track important information, such as package version, genome build, 
>> etc.
>
> In fact, hacking the function makecdfenv would not be difficult,
> but then what about version number, etc... ? The current
> "automagic" loading of the CDF-package (after downloading whenever
> necessary) calls for a package name, and very likely will pick
> the first one in the library path.
>
> If you want to archive/share your CDF environment, you can always
> attach an attribute with comments (note that the class CdfEnvAff
> has already slots to help with that).
>
> Otherwise, the help for "packages.skeleton" could give you hints on
> how to proceed.
>
> Hoping this helps,
> L.
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