[R-SIG-Mac] Does preprocessCore do ppc64?
Simon Urbanek
simon.urbanek at r-project.org
Fri Dec 14 20:15:17 CET 2007
Ah, well, that's the problem when you live on the cutting edge ;).
There is one more issue - the Leopard build uses gcc-4.2 from Apple.
Unfortunately it's not part of Xcode 3.0 :/. There are three ways to
fix this:
a) get gcc42preview1.dmg from Apple if you have ADC membership that
includes previews.
b) if you don't, you can install my build of gcc-42 from the R for Mac
pages. It is similar, but not the same. However, use at your own risk.
c) force R to use gcc-4.0. The easiest is probably to run this in
Terminal:
sudo ln -sfh gcc-4.0 /usr/bin/gcc-4.2
sudo ln -sfh g++-4.0 /usr/bin/g++-4.2
a) is best if you have access to it, c) is least invasive and can be
undone by
sudo rm /usr/bin/gcc-4.2 /usr/bin/g++-4.2
Sorry, I forgot about this issue when responding earlier.
I can only repeat that this all is all experimental, we hope to have a
more streamlined Leopard 64-bit support for R 2.7.0 including the GUI
etc. Also using 64-bit is not necessarily better - it is a bit slower
and pays off only with enough RAM (5-16GB).
Cheers,
Simon
On Dec 14, 2007, at 12:04 PM, Loren Engrav wrote:
> So my attempt to 64bit build failed, am so sorry
>
>> biocLite("simpleaffy", type="source")
> 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/src/contrib/simpleaffy_2.14.05.ta
> r.gz'
> Content type 'application/x-gzip' length 567142 bytes (553 Kb)
> opened URL
> ==================================================
> downloaded 553 Kb
>
> /Library/Frameworks/R.framework/Resources/library
> * Installing *source* package 'simpleaffy' ...
> ** libs
> ** arch - ppc64
> gcc-4.2 -arch ppc64 -std=gnu99 -no-cpp-precomp
> -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/ppc64
> -I/usr/local/include -fPIC -g -O2 -c simpleaffy.c -o simpleaffy.o
> /bin/bash: gcc-4.2: command not found
> make: *** [simpleaffy.o] Error 127
> chmod:
> /Library/Frameworks/R.framework/Resources/library/simpleaffy/libs/
> ppc64/*:
> No such file or directory
> ERROR: compilation failed for package 'simpleaffy'
> ** Removing '/Library/Frameworks/R.framework/Resources/library/
> simpleaffy'
> ** Restoring previous
> '/Library/Frameworks/R.framework/Resources/library/simpleaffy'
>
> The downloaded packages are in
> /private/tmp/RtmpWzr4jD/downloaded_packages
> Updating HTML index of packages in '.Library'
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,
> :
> installation of package 'simpleaffy' had non-zero exit status
>
>
>
>
> Please recall in preparation for this I did
>
> Previously installed (will change to R-devel later to get Quartz and
> R.app)
>>> R-2.6-branch
>>> R 2.6.1 Patched (2007-12-13)
>
> installed
>>> Xcode 3 from the Leopard DVD and
>>> GNU Fortan 4.2.1 and
>>> LaTeX
>>> And did in Terminal...
>>> export PATH=$PATH:/usr/local/bin and
>>> curl -s -S http://r.research.att.com/readline-5.2-1-quad.tar.gz|
>>> sudo tar fxz
> - -C / and
>>> curl -s -S http://r.research.att.com/jpegpng-quad.tar.gz|sudo tar
>>> fxz - -C /
>
> And to fire up did
>>> sudo R --arch="ppc64"
>
> And sessionInfo say
>> sessionInfo()
> R version 2.6.1 Patched (2007-12-12 r43661)
> powerpc-apple-darwin9.0.0
>
> locale:
> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> loaded via a namespace (and not attached):
> [1] rcompgen_0.1-17 tools_2.6.1
>
> And .Platform say
>> .Platform$r_arch
> [1] "ppc64"
>>
>
> And version say
>> 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)
>
> And echo say
> Loren-Engravs-Dual-G5:bin engrav$ echo $PATH
> /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/usr/X11/bin
>
> There is gfortran-4.2 in /usr/local/bin
>
> All on Leopard 10.5.1 and G5 dual 2gh ppc
>
> There are a bizillion google pages about
>>> /bin/bash: gcc-4.2: command not found
>>> make: *** [simpleaffy.o] Error 127
>
> How to fix this on this system?
>
> Thank you
>
>
> --
> Loren Engrav
> Univ Washington
> Seattle
>
>
>
>
>
>
>
>> From: Simon Urbanek <simon.urbanek at r-project.org>
>> Date: Fri, 14 Dec 2007 09:54:15 -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 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
>>>
>>>
>>
>
> _______________________________________________
> 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