[R-sig-Debian] Update to 2.8 and problem with liblapack

[Matthieu Stigler]

Hello

Reinstalling with apt-get did not work (same message error) but proper 
compiling from source was ok! I had the same problem with package minpack.lm

Thank for your help!


PS Dirk: I wrote an other message to the list without having subscribed, 
so email is probably waiting for approbation. Should I wait or resend it 
as list-member?


> 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!
>   

PS Sebastian: the friend who introduced me to Linux and installed the 
distribution was himself on Debian but choosed Ubuntu for a newbie...



Dirk Eddelbuettel a écrit :
> 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 dépendances       
> | > Lecture des informations d'état... Fait
> | > Les paquets supplémentaires suivants seront installés :
> | >   libblas-dev liblapack-dev r-base-core tcl8.5 tk8.5
> | > Paquets suggérés :
> | >   cdbs
> | > Les paquets suivants seront ENLEVÉS :
> | >   refblas3-dev
> | > Les NOUVEAUX paquets suivants seront installés :
> | >   libblas-dev liblapack-dev tcl8.5 tk8.5
> | > Les paquets suivants seront mis à jour :
> | >   r-base-core r-base-dev
> | > 2 mis à jour, 4 nouvellement installés, 1 à enlever et 19 non mis à 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
>
>