Re: [R] 64-bit R on Mac OS X 10.5.4

From: joseph <jdsandjd_at_yahoo.com>
Date: Sun, 27 Jul 2008 12:39:08 -0700 (PDT)

Hi Matt
Your method is the easiest way for me to install the 64-bit R. I followed the directions on your web site and then did the following: R --arch=x86_64
source("
http://bioconductor.org/biocLite.R") biocLite(type = "source",lib = "/Library/Frameworks/R.framework/Versions/2.8/Resources/RLib64")

I got many errors and warnings which I copied to the attached file. Any suggestions on how to fix the errors will be appreciated. Thank you for your help
Joseph

> sessionInfo()

R version 2.8.0 Under development (unstable) (2008-07-24 r46120) i386-apple-darwin9.4.0
locale:
en_US.UTF-8/en_US.UTF-8/C/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] tools_2.8.0

This is the computer I am using:
Hardware Overview:
  Model Name: Mac Pro
  Model Identifier: MacPro1,1
  Processor Name: Dual-Core Intel Xeon   Processor Speed: 2.66 GHz
  Number Of Processors: 2
  Total Number Of Cores: 4
  L2 Cache (per processor): 4 MB
  Memory: 20 GB
  Bus Speed: 1.33 GHz
  Boot ROM Version: MP11.005C.B08
  SMC Version: 1.7f10
  Serial Number: G87052SGUPZ

System Software Overview:
  System Version: Mac OS X 10.5.4 (9E17)   Kernel Version: Darwin 9.4.0
  Boot Volume: Macintosh HD
  Boot Mode: Normal

Hi Joseph,

For what it is worth (which might not be that much!), I have written down step by step instructions on my website for getting 64 bit R working under Leopard - it should be much different with Tiger: http://www.matthewckeller.com/html/64_bit_r_on_mac.html. I think it'll work but there may be some mistakes in there. I'd be happy to take suggestions...

Matt

On Fri, Jul 25, 2008 at 7:23 PM, Steven McKinney <smckinney_at_bccrc.ca> wrote:
>
> Hello
>
> I haven't found better instructions, it's just
> not an easy thing to do.
>
> You might also consider joining the r-sig-mac group
> and reviewing threads there for additional information.
>
> Rather than try to configure, make and install with
> one giant command, I'd suggest breaking the task down
> until you have worked out all the details. Then you
> can build more routinely with giant commands such as
> the one you report below.
>
> Note that the page of the URL you posted says this:
> "R on Mac OS X 10.5 (Leopard)"
>
> so look around the r.research.att.com
> website for older 10.4 related instructions.
> OS X 10.5 is different enough from 10.4 that
> copying and pasting the 10.5 instructions
> will not work everywhere.
>
> You don't say what kind of computer you have
> (Intel or PowerPC), if you have a power pc
> then -arch x86_64 is not right. So do
> report your hardware configuration as well
> as your operating system configuration.
>
> Try breaking up the build process into steps
> and review the messages generated at each step.
>
> e.g. the configure step: Just do these bits
>
> cd rd64
> ../R-devel/configure SHELL='/bin/bash' \
> r_arch=x86_64 \
> CC="gcc -arch x86_64 -std=gnu99" \
> CXX="g++ -arch x86_64" \
> OBJC="gcc -arch x86_64" \
> F77="gfortran -arch x86_64" \
> FC="gfortran -arch x86_64" \
> --with-system-zlib \
> --with-blas='-framework vecLib' \
> --with-lapack 1> configure.R.txt 2>&1
>
> The end bits of this version of the
> configure command redirect output and
> error messages to a file that you can then
> read, to see which bits you are missing and
> which bits cause problems. It's tough to catch those
> as they scroll by in a terminal window.
>
> If configure runs without any signs of trouble,
> try the make.
>
> make 1> make.R.txt 2>&1
>
> Then you can review all the make output for signs
> of problems and error messages.
>
>
> Here's a configure command that worked for me to
> build a 64-bit R on 10.4 a while back:
>
>
> ./configure --host=powerpc64-apple-darwin8.10.0 --build=powerpc64-apple-darwin8.10.0 \
> --prefix=/usr/local/lib64 'CC=gcc-4.0 -arch ppc64' 'CXX=g++ -arch ppc64' \
> 'FC=gfortran-4.0 -arch ppc64' 'F77=gfortran-4.0 -arch ppc64' \
> 'CFLAGS=-g -O3 -mtune=G5 -mcpu=G5' 'FFLAGS=-g -O3 -mtune=G5 -mcpu=G5' \
> 'LDFLAGS=-arch ppc64 -m64 -L/usr/local/lib' 'CXXFLAGS=-g -O3 -mtune=G5 -mcpu=G5' \
> 'FCFLAGS=-g -O3 -mtune=G5 -mcpu=G5' --disable-R-framework --enable-R-shlib \
> '--with-blas=-framework vecLib' --with-lapack --without-iconv 1> configure.R.txt 2>&1
>
>
> and also note that you need to have root privileges when doing the
> make install, so you either need to run the command as root
> (not so common on Mac OS X) or run
>
> sudo make install
>
> and enter your password etc.
>
> HTH
>
> Steve McKinney
>
>
>
>
> -----Original Message-----
> From: r-help-bounces_at_r-project.org on behalf of joseph
> Sent: Fri 7/25/2008 5:07 PM
> To: r-help_at_r-project.org
> Cc: r-help_at_r-project.org
> Subject: [R] 64-bit R on Mac OS X 10.4.5
>
> Hello
> I have a Mac OS X 10.4.5. I am trying to build a 64-bit R by following the directions on this page: http://r.research.att.com/building.html
>
> r_arch=x86_64 \
> CC="gcc -arch x86_64 -std=gnu99" \
> CXX="g++ -arch x86_64" \
> OBJC="gcc -arch x86_64" \
> F77="gfortran -arch x86_64" \
> FC="gfortran -arch x86_64"
>
> PATH=/usr/X11/bin:/usr/local/bin:$PATH
> export PATH
> LANG=C
> export LANG
> svn co https://svn.r-project.org/R/trunk R-devel
> # you may have to accept a certificate here
> cd R-devel
> tools/rsync-recommended
> cd ..
> # got the sources, on to building 64-bit R
> mkdir rd64
> cd rd64
> ../R-devel/configure SHELL='/bin/bash' \
> r_arch=x86_64 \
> CC="gcc -arch x86_64 -std=gnu99" \
> CXX="g++ -arch x86_64" \
> OBJC="gcc -arch x86_64" \
> F77="gfortran -arch x86_64" \
> FC="gfortran -arch x86_64" \
> --with-system-zlib \
> --with-blas='-framework vecLib' --with-lapack && \
> make -j4 && \
> make check && \
> make install
> cd ..when I try to run it by typing R, it gives me the following error: -bash: R: command not found
>
>
> Can any body help me to solve this problem or direct me to better step-by-step instructions.
> Thanks
> Joseph
>
>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help_at_r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> R-help_at_r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

-- 
Matthew C Keller
Asst. Professor of Psychology
University of Colorado at Boulder
www.matthewckeller.com



      

______________________________________________ R-help_at_r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Received on Sun 27 Jul 2008 - 19:52:03 GMT

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