Does preprocessCore do ppc64?

Thank you, maybe is coming into focus

Then I run R.app with options(arch="ppc64") in .Rprofile
That is a really bad idea (see the response you got previously).

Would appear that I have proven what you say is true

I bet you didn't install the package from sources. CRAN/BioC offer  
32-
bit package binaries only, so you have to install all packages from
sources (i.e. you must use type='source' in install.packages). Also
you need all the necessary tools for this (please read the page you
got the binaries from).

Couple lines up I included

source("http://bioconductor.org/biocLite.R")
biocLite("preprocessCore")

Again proving you correct

And I see the directions on <http://r.research.att.com/> are  
changing which
is good for R/Bio R1's

So now what I wish to do is 64bit Readaffy
And can use 64bit command line which is painful but would work
But have no 64bit Bio packages

As I understand now
To get 64bit R.app I must get the tools and build it
To get 64bit Bio packages I must get the tools and build them

I might try this being this deep into this and finding it rather fun

One question before I start
You say

note that R 2.6.1 doesn't have Quartz support in 64-bit, so the GUI
won't be of much use. You have to use R-devel for Quartz in 64-bit.

This means that from <http://r.research.att.com/>

R-2.6-branch
R 2.6.1 Patched (2007-12-12)

Will not work, I MUST use

R-devel
R 2.7.0 Under development
(unstable) (2007-12-12)

True? Even tho neither include R.app?

In preparation for this I have installed
Xcode 3 from the Leopard DVD
And
GNU Fortan 4.2.1

And
Will install LaTeX after massive download done

And did in Terminal...
export PATH=$PATH:/usr/local/bin
and
curl -s -S http://r.research.att.com/readline-5.2-1-quad.tar.gz|sudo  
tar fxz
- -C /
and
curl -s -S http://r.research.att.com/jpegpng-quad.tar.gz|sudo tar  
fxz - -C /

And of course, maybe I should bag it, admit I am over my head, and  
let some
"expert" with dChip do it

But then what the hell? Why not try it, if you can tolerate my  
questions
that is, and I am closer to ReadAffy 64bit 81 cell as I now have  
command
line 64bit R

From: Simon Urbanek <simon.urbanek at r-project.org>
Date: Thu, 13 Dec 2007 19:39:52 -0500
To: Loren Engrav <engrav at u.washington.edu>
Cc: "r-sig-mac at stat.math.ethz.ch" <r-sig-mac at stat.math.ethz.ch>
Subject: Re: [R-SIG-Mac] Does preprocessCore do ppc64?


On Dec 13, 2007, at 5:58 PM, Loren Engrav wrote:

Thank you, was helpful, is complicated for this geezer, but
interesting

The whole goal is to ReadAffy() on 81 chips which seems to need 64
bit to
avoid "cannot allocate vector...." error (or reduce chips or analyze
in
pieces but not yet ready to give up on this)

Other advisors advised

"Install Leopard 10.5.1

Now install either
  R-2.6-branch-leopard-universal.tar.gz
or
  R-devel-leopard-universal.tar.gz
depending on which version of BioC you want to use: the former is
for BioC
2.1 (the current release) and the latter for BioC 2.2 (the current
devel).

Then start R with --arch=ppc64 and you will be running in 64-bit
mode."

So I installed Leopard and R-2.6-branch and start with R -- 
arch=ppc64

=========
and as you suggested while running Command Line

version

             _
platform       powerpc-apple-darwin9.0.0
arch           powerpc
os             darwin9.0.0
system         powerpc, darwin9.0.0
status         Patched
major          2
minor          6.1
year           2007
month          12
day            12
svn rev        43661
language       R
version.string R version 2.6.1 Patched (2007-12-12 r43661)

.Machine$sizeof.pointer == 8

[1] TRUE

R.version$arch

[1] "powerpc"

.Platform$r_arch

[1] "ppc64"

============
Then I run R.app with options(arch="ppc64") in .Rprofile

That is a really bad idea (see the response you got previously). You
cannot change the architecture in a running R and you also cannot use
32-bit R.app with 64-bit R. If you want 64-bit R and the GUI, you  
have
to use 64-bit R.app (which you have to build from the sources). Also
note that R 2.6.1 doesn't have Quartz support in 64-bit, so the GUI
won't be of much use. You have to use R-devel for Quartz in 64-bit.

And get

version

             _
platform       powerpc-apple-darwin9.1.0
arch           powerpc
os             darwin9.1.0
system         powerpc, darwin9.1.0
status         Patched
major          2
minor          6.1
year           2007
month          12
day            12
svn rev        43661
language       R
version.string R version 2.6.1 Patched (2007-12-12 r43661)

.Machine$sizeof.pointer == 8

[1] FALSE

R.version$arch

[1] "powerpc"

.Platform$r_arch

[1] "ppc"

So would then seem at Command Line I have 64 but in R.app I do not

============
Then I try biocLite("preprocessCore") at Command Line and returns

.Platform$r_arch

[1] "ppc64"

sessionInfo()

R version 2.6.1 Patched (2007-12-12 r43661)
powerpc-apple-darwin9.0.0

locale:
en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] rcompgen_0.1-17

source("http://bioconductor.org/biocLite.R")
biocLite("preprocessCore")

Running biocinstall version 2.1.8 with R version 2.6.1
Your version of R requires version 2.1 of Bioconductor.
trying URL
'http://bioconductor.org/packages/2.1/bioc/bin/macosx/universal/contrib/2.6/
preprocessCore_1.0.0.tgz'
Content type 'application/x-gzip' length 157468 bytes (153 Kb)
opened URL
==================================================
downloaded 153 Kb


The downloaded packages are in

/var/folders/-O/-O2rx2VN2RWJgU+8ZMxMx++++TI/-Tmp-//RtmpHcRo5R/
downloaded_pac
kages

library(preprocessCore)

Error: package 'preprocessCore' is not installed for 'arch=ppc64'

I bet you didn't install the package from sources. CRAN/BioC offer  
32-
bit package binaries only, so you have to install all packages from
sources (i.e. you must use type='source' in install.packages). Also
you need all the necessary tools for this (please read the page you
got the binaries from).

Cheers,
Simon

===============
Then I try same with R.app and returns

.Platform$r_arch

[1] "ppc"

sessionInfo()

R version 2.6.1 Patched (2007-12-12 r43661)
powerpc-apple-darwin9.1.0

locale:
en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

source("http://bioconductor.org/biocLite.R")
biocLite("preprocessCore")

Running biocinstall version 2.1.8 with R version 2.6.1
Your version of R requires version 2.1 of Bioconductor.
trying URL
'http://bioconductor.org/packages/2.1/bioc/bin/macosx/universal/contrib/2.6/
preprocessCore_1.0.0.tgz'
Content type 'application/x-gzip' length 157468 bytes (153 Kb)
opened URL
==================================================
downloaded 153 Kb


The downloaded packages are in

/var/folders/-O/-O2rx2VN2RWJgU+8ZMxMx++++TI/-Tmp-//Rtmp3VK9Rw/
downloaded_pac
kages

library(preprocessCore)

Error in dyn.load(file, ...) :
unable to load shared library
'/Library/Frameworks/R.framework/Resources/library/preprocessCore/
libs/ppc/p
reprocessCore.so':

dlopen(/Library/Frameworks/R.framework/Resources/library/
preprocessCore/libs
/ppc/preprocessCore.so, 5): Library not loaded:
/Library/Frameworks/R.framework/Versions/2.6/Resources/lib/
libgfortran.2.dyl
ib
Referenced from:
/Library/Frameworks/R.framework/Resources/library/preprocessCore/
libs/ppc/pr
eprocessCore.so
Reason: image not found
Error in library(preprocessCore) : .First.lib failed for
'preprocessCore'

=============
So to me seems with your investigative advice
1) I have 64bit at command line
2) I do not have 64bit in R.app
3) preprocessCore is not 64bit (and other packages)

So I am closer to 64bit ReadAffy of 81 files but still not there

With your serious knowledge, how should I get to 64bit ReadAffy

Thank you

From: Prof Brian Ripley <ripley at stats.ox.ac.uk>
Date: Thu, 13 Dec 2007 17:00:36 +0000 (GMT)
To: Loren Engrav <engrav at u.washington.edu>
Cc: "r-sig-mac at stat.math.ethz.ch" <r-sig-mac at stat.math.ethz.ch>
Subject: Re: [R-SIG-Mac] Does preprocessCore do ppc64?

The short answer is that the BioC binary packages are not 64-bit.
But
then neither is the CRAN build of R 2.6.1 nor the CRAN binary
packages.

And very likely you are running a 32-bit R.

On Thu, 13 Dec 2007, Loren Engrav wrote:

I tried
options(arch="ppc64") in Rprofile
and seems to have worked,

I am sure it 'worked' for some value of 'worked', but what do you
think it
did?  You can't change the architecture of a running R process (and
you
need a running R process to use R code ...).  You find out whether
the
process is 64-bit by checking

.Machine$sizeof.pointer == 8

and R.version$arch will also indicate the architecture name (x86_64
on my
Macintel builds).

The sub-architecture (if any) of the running process is given by
.Platform$r_arch and the user cannot change it (it was set at
configure
time).  From the output below, that is 'ppc'.  Not only do the
architectures need to match, but do the sub-architecture settings:
this is
easy to achieve when building everything yourself, but not when
taking
binaries built on different systems by different people at  
different
times.

So, it seems

- you are running a 32-bit R.
- you are missing a Fortran library.

Please do try to deduce from the output what the problem is, not
guess and
never test your guesses.

I think R.app is ppc64 in Leopard

The CRAN build of 2.6.1 is not, and you haven't told us which build
you
are using.

AFAIK if you want 64-bit, you need to build packages from sources.

How to set all this up is AFAIK not fully documented, for the very
good
reason that it is *experimental*.  My understanding is that it is
intended
to support 64-bit MacOS binary builds from R 2.7.0 only.

But affy will not load as requires preprocessCore

Library(preprocessCore) returns

Error in dyn.load(file, ...) :
unable to load shared library
'/Library/Frameworks/R.framework/Resources/library/preprocessCore/
libs/ppc/p
reprocessCore.so':

dlopen(/Library/Frameworks/R.framework/Resources/library/
preprocessCore/libs
/ppc/preprocessCore.so, 5): Library not loaded:
/Library/Frameworks/R.framework/Versions/2.6/Resources/lib/
libgfortran.2.dyl
ib
Referenced from:
/Library/Frameworks/R.framework/Resources/library/preprocessCore/
libs/ppc/pr
eprocessCore.so
Reason: image not found
Error in library(preprocessCore) : .First.lib failed for
'preprocessCore'

I check libs in preprocessCore and find i386 and ppc, no ppc64

Does this mean preprocessCore as it stands does not do ppc64? Or I
am
getting the wrong one? Or I must build 64bit? Or?

The original thread is in Bio but this seems like a Mac specific
question

Thank you

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/ 
~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595