[R-SIG-Mac] Does preprocessCore do ppc64?
Loren Engrav
engrav at u.washington.edu
Fri Dec 14 22:15:16 CET 2007
me on the cutting edge? Hot damn
so I went to ADC and got gcc42preview1.dmg and installed same
then read in directions set target to process "C source files" using "GCC
4.2" and said damn, have no clue
then said, will ignore, and started up R and tried biocLite
and voila, PACKAGES ARE BEING INSTALLED, CAN YOU BELIEVE IT?
now I need affy to ReadAffy, but there are a bizillion dependencies laid
out in a large tree, and have been working down thru the tree having been
successful at maybe 10 files and have arrived at genefilter and this
returned
> biocLite("genefilter", 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/genefilter_1.16.0.tar
.gz'
Content type 'application/x-gzip' length 242543 bytes (236 Kb)
opened URL
==================================================
downloaded 236 Kb
/Library/Frameworks/R.framework/Resources/library
* Installing *source* package 'genefilter' ...
** libs
** arch - ppc64
g++-4.2 -arch ppc64 -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 half_range_mode.cpp -o
half_range_mode.o
powerpc-apple-darwin9-g++-4.2.1: unrecognized option '-no-cpp-precomp'
half_range_mode.cpp: In function Œdouble half_range_mode(double*, double*,
double, int)¹:
half_range_mode.cpp:101: warning: deprecated conversion from string constant
to Œchar*¹
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 init.c -o init.o
powerpc-apple-darwin9-gcc-4.2.1: unrecognized option '-no-cpp-precomp'
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 nd.c -o nd.o
powerpc-apple-darwin9-gcc-4.2.1: unrecognized option '-no-cpp-precomp'
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 pAUC.c -o pAUC.o
powerpc-apple-darwin9-gcc-4.2.1: unrecognized option '-no-cpp-precomp'
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 rowPAUCs.c -o rowPAUCs.o
powerpc-apple-darwin9-gcc-4.2.1: unrecognized option '-no-cpp-precomp'
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 rowttests.c -o rowttests.o
powerpc-apple-darwin9-gcc-4.2.1: unrecognized option '-no-cpp-precomp'
gfortran-4.2 -arch ppc64 -fPIC -g -O2 -c ttest.f -o ttest.o
g++-4.2 -arch ppc64 -dynamiclib -Wl,-headerpad_max_install_names
-Wl,-macosx_version_min -Wl,10.4 -undefined dynamic_lookup -single_module
-multiply_defined suppress -L/usr/local/lib -o genefilter.so
half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o
-lgfortran -lSystemStubs
-L/Library/Frameworks/R.framework/Resources/lib/ppc64 -lR -dylib_file
libRblas.dylib:/Library/Frameworks/R.framework/Resources/lib/ppc64/libRblas.
dylib
** R
** data
** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: survival
Loading required package: splines
Error in library.dynam(lib, package, package.lib) :
shared library 'RSQLite' not found
Calls: <Anonymous> ... loadNamespace -> namespaceImport -> loadNamespace ->
library.dynam
Execution halted
ERROR: lazy loading failed for package 'genefilter'
** Removing '/Library/Frameworks/R.framework/Resources/library/genefilter'
** Restoring previous
'/Library/Frameworks/R.framework/Resources/library/genefilter'
The downloaded packages are in
/private/tmp/Rtmpbv42ud/downloaded_packages
Updating HTML index of packages in '.Library'
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,
:
installation of package 'genefilter' had non-zero exit status
>
So say cannot find RSQLite
But installed.packages say
> installed.packages()
Package
AnnotationDbi "AnnotationDbi"
Biobase "Biobase"
Biostrings "Biostrings"
DBI "DBI"
DynDoc "DynDoc"
GO "GO"
KEGG "KEGG"
KernSmooth "KernSmooth"
MASS "MASS"
RColorBrewer "RColorBrewer"
ROC "ROC"
RSQLite "RSQLite"
affy "affy"
affyPLM "affyPLM"
affyQCReport "affyQCReport"
affydata "affydata"
affyio "affyio"
annaffy "annaffy"
annotate "annotate"
base "base"
boot "boot"
class "class"
cluster "cluster"
codetools "codetools"
datasets "datasets"
foreign "foreign"
gcrma "gcrma"
genefilter "genefilter"
geneplotter "geneplotter"
grDevices "grDevices"
graphics "graphics"
grid "grid"
hgu95av2 "hgu95av2"
lattice "lattice"
limma "limma"
marray "marray"
matchprobes "matchprobes"
methods "methods"
mgcv "mgcv"
multtest "multtest"
nlme "nlme"
nnet "nnet"
preprocessCore "preprocessCore"
rcompgen "rcompgen"
rpart "rpart"
simpleaffy "simpleaffy"
spatial "spatial"
splines "splines"
stats "stats"
stats4 "stats4"
survival "survival"
tcltk "tcltk"
tools "tools"
utils "utils"
vsn "vsn"
xtable "xtable"
with an RSQLite listed
so if RSQLite is present, why can't biocLite find it?
or have I missed something?
> 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
>
> .Platform$r_arch
[1] "ppc64"
>
--
Loren Engrav
Univ Washington
Seattle
> From: Simon Urbanek <simon.urbanek at r-project.org>
> Date: Fri, 14 Dec 2007 14:15:17 -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?
>
> 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
>>>>>>
>>>>>> _______________________________________________
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>>>>>> R-SIG-Mac at stat.math.ethz.ch
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>>
>>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> R-SIG-Mac mailing list
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>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>
>>>>
>>>
>>
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