[R-sig-Debian] (Current) Ubuntu : r-base-dev seems incompatible with atlas-base-dev.

[Dirk Eddelbuettel]

Emmanuel,

On 30 August 2008 at 00:04, Emmanuel Charpentier wrote:
| Dear list,
| 
| Setup : Ubuntu Hardy + updates + backports + security + R repository on
| a 3.2 GHz PIV dual-core processor.
| 
| Bitten (again...) by the "I'll optimize my setup" bug, I tried to test
| atlas. Following Dirk's advice on a not-so-recent post to R-help, I
| tried "apt-get install -s atlas3-doc atlas3-base-dev" (I tend to
| recompile some packages, so I need r-base-dev and I *think* I need
| atlas3-base-dev to allow the recompiled packages to use it, but I might
| be completely wrong...). Ahem ... :
| 
| [ Snip... ]
| 
| Les paquets suivants seront ENLEVÉS :
|   libblas-dev liblapack-dev r-base-dev
| 
| [ Snip again ... ]
| 
| (for non-francophones : "The following packages will be REMOVED : ...").
| 
| However, atlas3-base *is* currently installed, and I never had problems
| recompiling packages.

Quick guess: you have the old atlas-* packages instead of the new libatlas-*
packages. Try 

	$ sudo apt-get install libatlas3gf-base libatlas-base-dev

| So, my (first) question is : what would be the benefits of installing
| atlas3-base-dev ? Isn't that necessary for recompiling packages ?

[Make that libatlas-base-dev]  So that you can compile against Atlas and get
the 'automatically tuned linear algebra system' for better performance on
linear algebra.

| Second question : what would be the benefits/drawbacks of "apt-get
| install atlas3-sse2 lapack3" ? A brief test seems to hint to limited
| benefits...

[Make that libatlas3gf-sse2]  Faster performance for binary code tuned to
your process.  Atlas actually provides lapack, and replace it in use.

| Last but not least : Atlas does not seem to exist on other architectures
| (I'm interested in amd64, of course...), at least in Debian and Ubuntu.
| Are there similar projects for amd64 I'm not aware of ?

Are you sure?  This has built on many architectures for many years, and the
reason it took so long to get to libatlas [ie the new build with the new
Fortran compuler] was as far as I know the darn portability.

All this works on my Debian (which gets R from my Debian packages) and Ubuntu
(which gets R from CRAN) machines.

Hope this helps, Dirk

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