[R-SIG-Mac] Does preprocessCore do ppc64?

Simon Urbanek simon.urbanek at r-project.org
Fri Dec 14 01:39:52 CET 2007 

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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