[BioC] CDF environment for a custom Affy chip

[Henrik Bengtsson]

On 5/31/06, Seth Falcon <sfalcon at fhcrc.org> wrote:
> [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).

I've got a fairly generic RCMDprompt.bat script, which opens a Windows
Command prompt with PATH etc setup.  It assumes default installation
paths for many of the tools, and it figures out (from the Windows
Registry) where the R installation lives.  Thus, if everything works
as planned you should be able to just double click the script and get
a working environment for building packages, given that you have
installed all tools that is (see script for instructions).  Download:
http://www.maths.lth.se/help/R/RCMDprompt.bat

/Henrik

> > 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
>
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