[R-SIG-Mac] Does preprocessCore do ppc64?
Loren Engrav
engrav at u.washington.edu
Fri Dec 14 05:29:02 CET 2007
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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