[R-sig-Debian] trouble installing building packages from source using R 2.6.0 on Ubuntu Gutsy AMD64

[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

-- 
Three out of two people have difficulties with fractions.