R SIG Debian - Nov 2008 - Update to 2.8 and problem with liblapack

Hello

To update from R 2.6 to 2.8 (on Ubuntu 8.04 both) I had to install new 
tcl and liblapack packages (excuse me it is in french):
>  sudo apt-get install r-base-dev
> Lecture des listes de paquets... Fait
> Construction de l'arbre des d?pendances       
> Lecture des informations d'?tat... Fait
> Les paquets suppl?mentaires suivants seront install?s :
>   libblas-dev liblapack-dev r-base-core tcl8.5 tk8.5
> Paquets sugg?r?s :
>   cdbs
> Les paquets suivants seront ENLEV?S :
>   refblas3-dev
> Les NOUVEAUX paquets suivants seront install?s :
>   libblas-dev liblapack-dev tcl8.5 tk8.5
> Les paquets suivants seront mis ? jour :
>   r-base-core r-base-dev
> 2 mis ? jour, 4 nouvellement install?s, 1 ? enlever et 19 non mis ? jour.
It installed libblas-dev liblapack-dev and removed refblas3-dev.

I'm now unable to run the Matrix library, whatever I install it from 
within R or with apt-get, it claims a problem:
> library(Matrix)
> Loading required package: lattice
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>   unable to load shared library
'/usr/lib/R/site-library/Matrix/libs/Matrix.so':
>   libRlapack.so: cannot open shared object file: No such file or directory
> Error: package/namespace load failed for 'Matrix'
but there is a file Natrix.so in this directory (but no libRlapack.so)

Do you see where the problem is? Was I right to update R in this manner?

Thanks!

Matthieu

Hi,

I remember this was a problem with some packages a while back in Debian.
It has now been fixed, but I don't know about Ubuntu.

BTW, may I ask what all the fuss is about Ubuntu?  Why are so many
people so hyped about it and prefer it over Debian?  Note: this is not
bait for distro wars, just genuine curiosity.  Excuse the tangential OT!


Seb



On Sat, 15 Nov 2008 12:36:39 +0530,
Matthieu Stigler <matthieu.stigler at gmail.com> wrote:
> Hello To update from R 2.6 to 2.8 (on Ubuntu 8.04 both) I had to
> install new tcl and liblapack packages (excuse me it is in french):
>> sudo apt-get install r-base-dev Lecture des listes de paquets... Fait
>> Construction de l'arbre des d?pendances Lecture des informations
>> d'?tat... Fait Les paquets suppl?mentaires suivants seront
install?s
>> : libblas-dev liblapack-dev r-base-core tcl8.5 tk8.5 Paquets sugg?r?s
>> : cdbs Les paquets suivants seront ENLEV?S : refblas3-dev Les
>> NOUVEAUX paquets suivants seront install?s : libblas-dev
>> liblapack-dev tcl8.5 tk8.5 Les paquets suivants seront mis ? jour :
>> r-base-core r-base-dev 2 mis ? jour, 4 nouvellement install?s, 1 ?
>> enlever et 19 non mis ? jour.
> It installed libblas-dev liblapack-dev and removed refblas3-dev.
> I'm now unable to run the Matrix library, whatever I install it from
> within R or with apt-get, it claims a problem:
>> library(Matrix) Loading required package: lattice Error in
>> dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared
>> library '/usr/lib/R/site-library/Matrix/libs/Matrix.so':
>> libRlapack.so: cannot open shared object file: No such file or
>> directory Error: package/namespace load failed for 'Matrix'
> but there is a file Natrix.so in this directory (but no libRlapack.so)
> Do you see where the problem is? Was I right to update R in this
> manner?
> Thanks!
> Matthieu


-- 
Seb

On 15 November 2008 at 12:36, Matthieu Stigler wrote:
| Hello
| 
| To update from R 2.6 to 2.8 (on Ubuntu 8.04 both) I had to install new 
| tcl and liblapack packages (excuse me it is in french):
          ^^^^^^^^^

| >  sudo apt-get install r-base-dev
| > Lecture des listes de paquets... Fait
| > Construction de l'arbre des d?pendances       
| > Lecture des informations d'?tat... Fait
| > Les paquets suppl?mentaires suivants seront install?s :
| >   libblas-dev liblapack-dev r-base-core tcl8.5 tk8.5
| > Paquets sugg?r?s :
| >   cdbs
| > Les paquets suivants seront ENLEV?S :
| >   refblas3-dev
| > Les NOUVEAUX paquets suivants seront install?s :
| >   libblas-dev liblapack-dev tcl8.5 tk8.5
| > Les paquets suivants seront mis ? jour :
| >   r-base-core r-base-dev
| > 2 mis ? jour, 4 nouvellement install?s, 1 ? enlever et 19 non mis ? jour.
| It installed libblas-dev liblapack-dev and removed refblas3-dev.
| 
| I'm now unable to run the Matrix library, whatever I install it from 
| within R or with apt-get, it claims a problem:
| 
| > library(Matrix)
| > Loading required package: lattice
| > Error in dyn.load(file, DLLpath = DLLpath, ...) :
| >   unable to load shared library
'/usr/lib/R/site-library/Matrix/libs/Matrix.so':
| >   libRlapack.so: cannot open shared object file: No such file or
      ^^^^^^^^^^^^^
| > directory

| > Error: package/namespace load failed for 'Matrix'
| 
| but there is a file Natrix.so in this directory (but no libRlapack.so)
| 
| Do you see where the problem is? Was I right to update R in this manner?

Short story: You did nothing wrong, but you now need to update / reinstall
your matrix package as it is a user of lapack.

The long story is that Debian finally switched from an older to a newer atlas
/ lapack which allowed us to change how R uses lapack. It uses to be internal
(hence libRlapack.so indicating R's sources for lapack function), it is now
using the system-wide package.  So for that you need to install the matching
Matrix package (ie 'sudo apt-get install r-cran-matrix) or rebuild one
yourself.

Hth, Dirk

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