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:[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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