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.
Cheers,
Patrick
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:[EMAIL PROTECTED]
Sent: Thu 11/6/2008 2:58 PM
To: Steven McKinney
Cc: R-SIG-Mac@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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