[R-SIG-Mac] Does preprocessCore do ppc64?
Loren Engrav
engrav at u.washington.edu
Fri Dec 14 18:04:15 CET 2007
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
>>>>
>>>>
>>>
>>
>> _______________________________________________
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