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

[Simon Urbanek]

On Nov 6, 2008, at 7:24 PM, Patrick Aboyoun wrote:

> Steve and Steve,
> While this is slightly off topic, I would just like to offer a brief  
> aside since Bioconductor has been brought up on this mailing list.  
> The Bioconductor project doesn't support ppc64 at this time and that  
> is why I was silent on it in my e-mail to the Bioconductor  
> community. We currently have only one Mac OS X 10.5 (Leopard) build  
> machine and it uses Intel technology. The reason why some of the  
> BioC 2.3 packages have ppc64 binaries and some don't is because some  
> packages with external source code let R fully control the compiler  
> flags (like the one specifying the architecture) and others don't  
> (e.g. because they include a make framework). For the ones that R  
> has complete compiler flag control over, the BioC 2.3 Mac OS X  
> Leopard packages contain all four architectures since we use Simon  
> Urbanek's R binaries that contain quad-architecture support as well  
> as the compilers he recommends. When R doesn't have full control  
> over the compilation flags, we use a standard R-based compilation  
> method to create the libraries that are appropriate for ppc, i386,  
> x86_64. If there are others out there who are in the same boat as  
> Steve McKinney and would like to use BioC 2.3 on a ppc64 and are  
> having trouble doing so, let me know so I can pass that information  
> on to the BioC core team.
>

This is slightly off-topic, but I could offer my ppc64 machine to  
build libraries for BioC binaries with configure script if that is  
desirable. According to the Mac survey there are very few ppc64  
machines with enough memory to warrant 64-bit R for ppc64, so it's  
still a questionable endeavor, but possible. (In fact I'm still not  
quite convinced that it's worth maintaining ppc64 binaries since G5 is  
now obsolete and next OS X reportedly won't support it anyway, but as  
long as I have a G5 in my office I'm simply keeping it in the chain).

Cheers,
Simon


>
>
> 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.
>>
>>
>> -----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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