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trouble installing building packages from source using R 2.6.0 on Ubuntu Gutsy AMD64

4 messages · Mark Kimpel, Dirk Eddelbuettel, Johannes Ranke +1 more

Original
Mark Kimpel
# 
I have recently upgraded to Ubuntu Gutsy and, for the first time, am 
using a 64-bit installation. After failing miserably to install R from 
source, not a problem for me in the past with a 32-bit install, I went 
the route of using the Debian Etch build. This went smoothly, but I am 
unable to update my numerous R and BioConductor packages, getting 
non-zero exit status errors on each package. Is there a repository of 
pre-built packages for Debian Etch 64 besides the r-base and 
r-recommended? If not, could someone suggest how I might get things 
working installing from source?

I have installed the ia32 library, which did help me build VMWare, but 
did not help with R. Reading the R-admin manual, there are some 
suggested compiler flags, but I don't know how to enter them as I am a 
relative new-comer to Linux.

Thanks so much,
Mark

---

Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

(317) 490-5129 Work, & Mobile & VoiceMail
(317) 663-0513 Home (no voice mail please)
Dirk Eddelbuettel
#
On 30 October 2007 at 11:26, Mark W Kimpel wrote:
| I have recently upgraded to Ubuntu Gutsy and, for the first time, am 
| using a 64-bit installation. After failing miserably to install R from 
| source, not a problem for me in the past with a 32-bit install, I went 
| the route of using the Debian Etch build. This went smoothly, but I am 

You mean you installed the .deb file from Debian onto Ubuntu?  Not something
I'd recommend....

IIRC we have backports for 64 bit, and we have backports for Ubuntu.  We just
don't have them for 64 Bit Ubuntu ...   

| unable to update my numerous R and BioConductor packages, getting 
| non-zero exit status errors on each package. Is there a repository of 
| pre-built packages for Debian Etch 64 besides the r-base and 
| r-recommended? If not, could someone suggest how I might get things 
| working installing from source?

At work, I use Ubuntu 32bit.  I simply have and entry for Debian _sources_:

foo:~> grep debian /etc/apt/sources.list
deb-src http://localhost:9999/ftp.debian.org/debian/ unstable main contrib non-free

(and please ignore the localhost bit, just my apt-proxy ...)   

Then it is just a matter of apt-get update; apt-get source r-base to fetch
the sources for a local rebuild / backport.  For Feisty, I need to modidy
debian/rules and debian/control to un-hardwire the choice of gcc 4.2 to just
gcc (and g++, gfortran).  We can help you with that; and the exisiting
backports have the _exact_ patch required.

After that, everything just works. I tend to install CRAN and BioC directly
into /usr/local which I then share over NFS.  No problems whatsoever. [ A
while back I needed a more recent graphviz from Debian but Gutsy may already
have that for you. ]

If all this is too much sys-admining for you, then you should consider
getting some local help.  We'll try to coach you from here but you do need to
some of the heavy lifting too.

Hth, Dirk
Johannes Ranke
# 
Hi Mark,

Did you try what is written at the very end of the READMEs

	http://cran.r-project.org/bin/linux/ubuntu/

and

	http://cran.r-project.org/bin/linux/debian/

i.e. install r-base-dev and then update the packages from within R?

Johannes

* Mark W Kimpel <mwkimpel at gmail.com> [071030 16:40]:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Vincent Goulet
    

    

      
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Le mar. 30 oct. ? 11:26, Mark W Kimpel a ?crit :

            

      
      
      
    

        
As Dirk mentioned, there aren't any binary packages of R for 64-bit  
Ubuntu. If you look up the archives of the list, you'll see that this  
subject has been discussed a few times already, but so far nobody has  
volunteered to maintain packages.

I cannot help you to build from source any further than pointing to  
the build scripts I use for the i386 packages. There you will see the  
changes (referred to by Dirk) I make to the Debian source packages so  
that they build on Ubuntu. See the Ubuntu README for details.

Vincent