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ubuntu hardy heron and lme4

4 messages · Michael Rutter, Dirk Eddelbuettel, Anne York

Original
Michael Rutter
# 
Anne,

The version of lme4 you find on the Hardy repositories is very old at 
this point.  Looking at the package information page 
(http://packages.ubuntu.com/hardy/r-cran-lme4) it was built using R 
2.5.1, which could be the cause of your problems.

My suggestion would be to use install.packages("lme4") from within R to 
make sure you have the latest version.  See 
http://cran.r-project.org/bin/linux/ubuntu/ for additional information.

Hope this helps,
Michael
On 02/28/2010 03:38 PM, Anne York wrote:

  
    

      
      
    

  


  


    

    

      
      

        


  

        

      Anne York
    

    

      
      #
    

  


  

      
Hi Michael:

I already tried reinstalling from with R on cran -- after 
checking on the status of LAPACK:

/usr/bin/R CMD config LAPACK_LIBS

to which the system responded 

-llapack

The result was the same. The programs within lme4 failed to 
compile because -llapack was not found. The error message 
during installation was: 

/usr/bin/ld: cannot find -llapack
collect2: ld returned 1 exit status

        
On Mon, 1 Mar 2010, Michael Rutter wrote:

        
MR > Anne,
MR > 
MR > The version of lme4 you find on the Hardy repositories is very old at this
MR > point.  Looking at the package information page
MR > (http://packages.ubuntu.com/hardy/r-cran-lme4) it was built using R 2.5.1,
MR > which could be the cause of your problems.
MR > 
MR > My suggestion would be to use install.packages("lme4") from within R to
MR > make sure you have the latest version.  See
MR > http://cran.r-project.org/bin/linux/ubuntu/ for additional information.
MR > 
MR > Hope this helps,
MR > Michael
MR >

        
MR > On 02/28/2010 03:38 PM, Anne York wrote:

        
MR > > I have R version 2.10.1 (2009-12-14)  installed on Ubuntu HH (version
MR > > 8.04)
MR > > 
MR > > I installed lme4 from the Ubuntu respository. When I executed the
MR > > library(lme4) command, R responds that lme4.so was not found.
MR > > 
MR > > I then uninstalled lme4 and tried again from cran. When the program
MR > > tried to compile, there was a message that -llapack could not be found,
MR > > so the package failed to install.
MR > > 
MR > > If I execute the following:
MR > > 
MR > > york at sasquatch:~$ /usr/bin/R CMD config LAPACK_LIBS
MR > > 
MR > > the system responds:
MR > > 
MR > > -llapack
MR > > 
MR > > I'm not sure where to go from here.
MR > > 
MR > > Is -llapack installed but R can't find it, eg, is there a faulty link
MR > > somewhere? Has anyone else had this problem and solved it?
MR > > 
MR > > Anne
MR > > 
MR > > _______________________________________________
MR > > R-SIG-Debian mailing list
MR > > R-SIG-Debian at r-project.org
MR > > https://stat.ethz.ch/mailman/listinfo/r-sig-debian
MR > 
MR > -- 
MR > Dr. Michael A. Rutter
MR > School of Science
MR > Penn State Erie, The Behrend College
MR > Station Road
MR > Erie, PA 16563
MR > http://math.bd.psu.edu/faculty/rutter
MR >

  
  


  


      

    

    

      
      

        


  

        

      Dirk Eddelbuettel
    

    

      
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On 1 March 2010 at 08:08, Anne York wrote:

        
| Hi Michael:
| 
| I already tried reinstalling from with R on cran -- after 
| checking on the status of LAPACK:
| 
| /usr/bin/R CMD config LAPACK_LIBS
| 
| to which the system responded 
| 
| -llapack
| 
| The result was the same. The programs within lme4 failed to 
| compile because -llapack was not found. The error message 
| during installation was: 
| 
| /usr/bin/ld: cannot find -llapack
| collect2: ld returned 1 exit status

Do 'dpkg -l | grep lapack' and make sure you see liblapack-dev as installed.

Also do 'ldd /usr/lib/R/bin/exec/R' and make sure you do _not_ have a depends
on Rlapack.so.  There was an important change in the Fortran compiler a while
back; I no longer anything as ancient as Ubuntu 8.04.  It may still date back
to those days...
  
Dirk

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Anne York
    

    

      
      #
    

  


  

      
On Mon, 1 Mar 2010, Dirk Eddelbuettel wrote:

        
DE >

        
DE > On 1 March 2010 at 08:08, Anne York wrote:

        
DE > | Hi Michael:
DE > | 
DE > | I already tried reinstalling from with R on cran -- after 
DE > | checking on the status of LAPACK:
DE > | 
DE > | /usr/bin/R CMD config LAPACK_LIBS
DE > | 
DE > | to which the system responded 
DE > | 
DE > | -llapack
DE > | 
DE > | The result was the same. The programs within lme4 failed to 
DE > | compile because -llapack was not found. The error message 
DE > | during installation was: 
DE > | 
DE > | /usr/bin/ld: cannot find -llapack
DE > | collect2: ld returned 1 exit status
DE > 
DE > Do 'dpkg -l | grep lapack' and make sure you see liblapack-dev as installed.
DE > 
DE > Also do 'ldd /usr/lib/R/bin/exec/R' and make sure you do _not_ have a depends
DE > on Rlapack.so.  There was an important change in the Fortran compiler a while
DE > back; I no longer anything as ancient as Ubuntu 8.04.  It may still date back
DE > to those days...
DE >   
DE > Dirk
DE > 


Thanks Dirk. that did the trick. I did not have the 
development version installed. 

Re the oldness of Ubuntu 8.04 -- These days I'm staying with 
LTS versions. 

Anne