[R-SIG-Mac] Does preprocessCore do ppc64?
Simon Urbanek
simon.urbanek at r-project.org
Fri Dec 14 15:54:15 CET 2007
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?
>
You don't have to, but you won't have Quartz graphics. You can still
use the command line and X11 graphics in R 2.6.1. You indicated that
you are interested in using R.app, so I just felt that I should warn
you ;).
> In preparation for this I have installed
> Xcode 3 from the Leopard DVD
> And
> GNU Fortan 4.2.1
That's all you really need. Everything else is optional.
>
> 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 /
>
Those are necessary for building R, but not for packages. However, it
doesn't hurt ;).
> 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
>
Yes :). Good luck.
I hope you have far more than 4GB of RAM in your machine, otherwise
the whole exercise is probably futile...
Unfortunately I'm short of machines, so I can't offer more binaries
for now ...
Cheers,
Simon
>> 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
>>>
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>
>>>
>>
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
>
More information about the R-SIG-Mac
mailing list