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Update to 2.8 and problem with liblapack

5 messages · Sébastien Bihorel, Matthieu Stigler, Dirk Eddelbuettel

Original
Matthieu Stigler
# 
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):
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:
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
Sébastien Bihorel
# 
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:

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Dirk Eddelbuettel
    

    

      
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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

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Matthieu Stigler
    

    

      
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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?

            

      
      
      
    

        
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 ?crit :

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Dirk Eddelbuettel
    

    

      
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On 16 November 2008 at 13:48, Matthieu Stigler wrote:

        
| Hello
| 
| Reinstalling with apt-get did not work (same message error) but proper 

That could then be an Ubuntu bug that they need to rebuild the distribution's
r-cran-matrix package.  Could you please follow-up and file an Ubuntu bug
report? 

| 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?

Resend as a subscriber, otherwise it will not come through. It may come
through eventually after weeks of delay, but that is probably not what you want.

Dirk