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

Patrick Aboyoun paboyoun at fhcrc.org
Fri Nov 7 01:24:13 CET 2008

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.


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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