[BioC] CDF environment for a custom Affy chip

[Seth Falcon]

[I goofed my original response and didn't cc the list.  With Oleg's
permission, I'm forwarding his response (with comments added)]


"Oleg Moskvin" <ovm at uwyo.edu> writes:
> Hi Seth,
>
> Thanks for the reply. The error message does not look too informative:
>
>
> -----------------------------------------------------------------
> C:\Program Files\R\R-2.3.0\bin>R CMD INSTALL uwyrhodo1acdf
>
> *** Installation of uwyrhodo1acdf failed ***
>
> Removing 'C:/PROGRA~1/R/R-23~1.0/library/uwyrhodo1acdf'
>
> C:\Program Files\R\R-2.3.0\bin>
> -----------------------------------------------------------------
>
> As you see, this is run from the "bin" directory of R. I've copied the
> folder generated by makecdfenv there. This may look weird but running
> it from other places (such as /library) results in not finding the R
> executable at all! See below.
>
> -----------------------------------------------------------------
> C:\Program Files\R\R-2.3.0\bin>R CMD INSTALL uwyrhodo1acdf
>
> *** Installation of uwyrhodo1acdf failed ***
>
> Removing 'C:/PROGRA~1/R/R-23~1.0/library/uwyrhodo1acdf'
>
> C:\Program Files\R\R-2.3.0\bin>
> -----------------------------------------------------------------

I think you copy/pasted the wrong thing for the second example.  But
your path issue is almost certainly the problem.  The chain of tools
required to build packages from their source directories on Windows is
quite particular; if you don't get things just right, it won't work.

> This looks like the "path" problem, but frankly, I do not now how to
> fix this in Windows XP (years ago I did edit this under DOS ;)).

We have a document that describes building R from source on Windows.
It is here: http://wiki.fhcrc.org/bioc/HowTo/Build_R_on_Windows

You may not need a complete source build for what you want to do on
Windows, but you _will_ need a complete and working tool chain.  The
link I've provided has details on this, including PATH stuff.

To set your PATH on Windows: right-click on My Computer, select
Properties, Advanced, Environment Variables (this is from memory, may
not be exactly right).

> As another possibility, I could supply the original cdf file, if it is
> possible to generate the cdf-environment remotely and then install it
> from zip file. BTW, several other laboratories would be interested in
> it (the Rhodobacter genechip will be commercially available soon).

Seems like you are close to getting things working, but we could
arrange to build the package if you can't get it working.

And if the result would be of general interest to folks, we can also
consider adding it to our hosted repository.

Best,

-- 
+ seth