[R-SIG-Mac] 64 bit - Installing packages from source

[Simon Urbanek]

On Nov 6, 2008, at 6:07 PM, Steven McKinney wrote:

>
> Prof. Ripley replied
>> Note that R 2.8.0 and Bioconductor 2.3 postdate the messages you  
>> quote.
> but I have not yet seen any announcement that it is no longer  
> necessary to install from sources, and Patrick Aboyoun does not  
> mention ppc64, so I'd still really appreciate guidance on this issue  
> for Mac OS X Leopard for arch ppc64.
>

You can use binary packages with the Leopard build. If some packages  
are not available or don't work, feel free to fall back to  
installation from sources. As for ppc64 there is still the issue of R  
not supporting cross-compilation, so packages with configure script  
are currently available for i386, ppc and x86_64 only. There is a plan  
to build dylibs on a ppc64 machine and merge them, but I didn't have  
time to set it up yet. There are a few remaining issues with the  
Leopard build that I'd like to address before putting it on CRAN  
officially which are mostly related to dependent libraries.

Cheers,
Simon


>
> -----Original Message-----
> From: Steve Lianoglou [mailto:mailinglist.honeypot at gmail.com]
> Sent: Thu 11/6/2008 2:58 PM
> To: Steven McKinney
> Cc: R-SIG-Mac at stat.math.ethz.ch
> Subject: Re: [R-SIG-Mac] 64 bit - Installing packages from source
>
>> "> You don't actually need to install bioconductor packages from
>> source  "
>>
>> Can Simon Urbanek weigh in on this?
>> I've been keeping an eye on R-SIG-Mac and have been seeing
>> repeated references in the last few weeks about
>> installing from source for 64-bit R.
>> ...
>
>
> For some tangential weight, see this posting where Patrick Aboyoun
> answered my question regarding using 64bit bioconductor on os x:
>
> http://thread.gmane.org/gmane.science.biology.informatics.conductor/20273/focus=20404
>
> As a point of reference, although he doesn't list ppc64 there, looking
> through my d/l'd bioconductor I see most all of the packages have
> ppc64 builds in their libs folders. The only one that doesn't have
> ppc64 is `affy`, which is curious.
>
> Given that limma and affy both d/l when you do a default BioC install
> with `biocLite()`, I'm not sure why that's the case.
>
> -steve
>
> --
> Steve Lianoglou
> Graduate Student: Physiology, Biophysics and Systems Biology
> Weill Medical College of Cornell University
>
> http://cbio.mskcc.org/~lianos
>
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