Does preprocessCore do ppc64?
Hi Loren,
it seems you have all the tools to build the packages.
So, this is what you need:
1) load R from the command line using the 64 bits mode
2) type: source("http://www.bioconductor.org/biocLite.R")
3) type, note the "type" argument:
biocLite(c("Biobase", "affy", "preprocessCore"), type="source")
this will download the *source*, compile and install (64 bits)....
because R is under /Library (I assume), you want to load R using "sudo"
sudo R --arch=ppc64
btw, you want to repeat the same procedure for other packages you
might need
b
On Dec 13, 2007, at 11:29 PM, Loren Engrav wrote:
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=$PATH:/usr/local/bin and curl -s -S http://r.research.att.com/readline-5.2-1-quad.tar.gz|sudo tar fxz - -C / and curl -s -S http://r.research.att.com/jpegpng-quad.tar.gz|sudo tar fxz - -C / And of course, maybe I should bag it, admit I am over my head, and let some "expert" with dChip do it But then what the hell? Why not try it, if you can tolerate my questions that is, and I am closer to ReadAffy 64bit 81 cell as I now have command line 64bit R -- Loren Engrav Univ Washington Seattle
From: Simon Urbanek <simon.urbanek at r-project.org> Date: Thu, 13 Dec 2007 19:39:52 -0500 To: Loren Engrav <engrav at u.washington.edu> Cc: "r-sig-mac at stat.math.ethz.ch" <r-sig-mac at stat.math.ethz.ch> Subject: Re: [R-SIG-Mac] Does preprocessCore do ppc64? On Dec 13, 2007, at 5:58 PM, Loren Engrav wrote:
Thank you, was helpful, is complicated for this geezer, but interesting The whole goal is to ReadAffy() on 81 chips which seems to need 64 bit to avoid "cannot allocate vector...." error (or reduce chips or analyze in pieces but not yet ready to give up on this) Other advisors advised "Install Leopard 10.5.1 Now install either R-2.6-branch-leopard-universal.tar.gz or R-devel-leopard-universal.tar.gz depending on which version of BioC you want to use: the former is for BioC 2.1 (the current release) and the latter for BioC 2.2 (the current devel). Then start R with --arch=ppc64 and you will be running in 64-bit mode." So I installed Leopard and R-2.6-branch and start with R -- arch=ppc64 ========= and as you suggested while running Command Line
version
_ platform powerpc-apple-darwin9.0.0 arch powerpc os darwin9.0.0 system powerpc, darwin9.0.0 status Patched major 2 minor 6.1 year 2007 month 12 day 12 svn rev 43661 language R version.string R version 2.6.1 Patched (2007-12-12 r43661)
.Machine$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
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