Skip to content

problems with Rcmdr on R-2.10.0 with Karmic Koala

7 messages · Michael Rutter, Dirk Eddelbuettel, Hodgess, Erin +1 more

Original
Michael Rutter
# 
Erin,

I don't have a machine running Karmic yet (I have learned never to 
update a linux distribution in the middle of the semester), so I can't 
test this easily.  At what point are you getting the MASS error?

Also, are you using the ubuntu packages on CRAN or the ones that come 
with Karmic in universe?

Michael
Hodgess, Erin wrote:

  
    

      
      
    

  


  


      

    

    

      
      

        
      

    

    

      
      

        


  

        

      Dirk Eddelbuettel
    

    

      
      #
    

  


  

      
On 23 November 2009 at 14:27, Hodgess, Erin wrote:

        
| Hi!
| 
| By using the "update.packages(checkBuilt=TRUE)" statement, I got rid of the MASS error.
| 
| I got the packages from the Berkeley CRAN repository.
| 
| But the Rcmdr menu screen is not appearing.  I think that there may be an issue with tcltk.

It's just a hunch: but by mixing packages and hand-compilation you may no
longer use all the library path entries. So 'your' R may not see the
libraries installed from 'our R' which use:

R> .libPaths()
[1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"       "/usr/lib/R/library"           
R> 

Run available.packages() and see if you get what you were expecting. It may
of course be something different alltogether...

Hth, Dirk

| Thanks,
| Erin
| 
| 
| Erin M. Hodgess, PhD
| Associate Professor
| Department of Computer and Mathematical Sciences
| University of Houston - Downtown
| mailto: hodgesse at uhd.edu
| 
| 
| 
| -----Original Message-----
| From: Michael Rutter [mailto:mar36 at psu.edu]
| Sent: Mon 11/23/2009 2:25 PM
| To: Hodgess, Erin
| Cc: r-sig-debian at r-project.org
| Subject: Re: [R-sig-Debian] problems with Rcmdr on R-2.10.0 with Karmic Koala
|  
| Erin,
| 
| I don't have a machine running Karmic yet (I have learned never to 
| update a linux distribution in the middle of the semester), so I can't 
| test this easily.  At what point are you getting the MASS error?
| 
| Also, are you using the ubuntu packages on CRAN or the ones that come 
| with Karmic in universe?
| 
| Michael
|

        
| Hodgess, Erin wrote:

        
| > Dear R Debian People:
| > 
| > I have put this on regular R help as well, but thought that I'd try here too.
| > 
| > I updated to R-2.10.0 on Ubuntu Karmic Koala via apt-get update, apt-get install.
| > 
| > Then I had a problem that said that I need MASS <= R-2.9.2.  Fair enough.  Uwe Ligges was kind enough to point out that I needed to use 
| >> update.packges(checkBuilt=TRUE)
| > 
| > So I did.
| > 
| > Now the menu on Rcmdr does not appear.
| > 
| > Just as an experiment, I downloaded the R-2.10.0.tar.gz file and installed via ./configure, make, etc. and all is well there.
| > 
| > Any help would be much appreciated.
| > 
| > Thanks,
| > Sincerely,
| > Erin
| > 
| > 
| > Erin M. Hodgess, PhD
| > Associate Professor
| > Department of Computer and Mathematical Sciences
| > University of Houston - Downtown
| > mailto: hodgesse at uhd.edu
| > 
| > 
| > 	[[alternative HTML version deleted]]
| > 
| > _______________________________________________
| > R-SIG-Debian mailing list
| > R-SIG-Debian at r-project.org
| > https://stat.ethz.ch/mailman/listinfo/r-sig-debian
| 
| -- 
| Dr. Michael A. Rutter
| School of Science
| Penn State Erie, The Behrend College
| Station Road
| Erie, PA 16563
| http://math.bd.psu.edu/faculty/rutter
| 
| 
| 	[[alternative HTML version deleted]]
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian

  
    

      
      
    

  


  


      

    

    

      
      

        
      

    

    

      
      

        


  

        

      Dirk Eddelbuettel
    

    

      
      #
    

  


  

      
On 23 November 2009 at 19:53, Hodgess, Erin wrote:

        
| Hi again.
| 
| Here is what I have in .libPaths()
| 
| > .libPaths()
| [1] "/home/erin/R/i486-pc-linux-gnu-library/2.10"
| [2] "/usr/local/lib/R/site-library"              
| [3] "/usr/lib/R/site-library"                    
| [4] "/usr/lib/R/library"                         
| >
| 
| Is the first entry throwing off the other ones, please?

That's for you to find out by running

       AP <- available.packages() 

and determining what you have in AP and what you expected there. Also, if you
have multiple installations of a package, an unqualified library(foo) that
does not give the lib.path will get the first one. That could be you problem.
Or maybe it's something else, but I doubt tcl/tk is to blame.

Dirk

| Thanks,
| Erin
| 
| 
| Erin M. Hodgess, PhD
| Associate Professor
| Department of Computer and Mathematical Sciences
| University of Houston - Downtown
| mailto: hodgesse at uhd.edu
| 
| 
| 
| -----Original Message-----
| From: Dirk Eddelbuettel [mailto:edd at debian.org]
| Sent: Mon 11/23/2009 4:44 PM
| To: Hodgess, Erin
| Cc: mar36 at psu.edu; r-sig-debian at r-project.org
| Subject: Re: [R-sig-Debian] problems with Rcmdr on R-2.10.0 with Karmic Koala
|  
|

        
| On 23 November 2009 at 14:27, Hodgess, Erin wrote:

        
| | Hi!
| | 
| | By using the "update.packages(checkBuilt=TRUE)" statement, I got rid of the MASS error.
| | 
| | I got the packages from the Berkeley CRAN repository.
| | 
| | But the Rcmdr menu screen is not appearing.  I think that there may be an issue with tcltk.
| 
| It's just a hunch: but by mixing packages and hand-compilation you may no
| longer use all the library path entries. So 'your' R may not see the
| libraries installed from 'our R' which use:
| 
| R> .libPaths()
| [1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"       "/usr/lib/R/library"           
| R> 
| 
| Run available.packages() and see if you get what you were expecting. It may
| of course be something different alltogether...
| 
| Hth, Dirk
| 
| | Thanks,
| | Erin
| | 
| | 
| | Erin M. Hodgess, PhD
| | Associate Professor
| | Department of Computer and Mathematical Sciences
| | University of Houston - Downtown
| | mailto: hodgesse at uhd.edu
| | 
| | 
| | 
| | -----Original Message-----
| | From: Michael Rutter [mailto:mar36 at psu.edu]
| | Sent: Mon 11/23/2009 2:25 PM
| | To: Hodgess, Erin
| | Cc: r-sig-debian at r-project.org
| | Subject: Re: [R-sig-Debian] problems with Rcmdr on R-2.10.0 with Karmic Koala
| |  
| | Erin,
| | 
| | I don't have a machine running Karmic yet (I have learned never to 
| | update a linux distribution in the middle of the semester), so I can't 
| | test this easily.  At what point are you getting the MASS error?
| | 
| | Also, are you using the ubuntu packages on CRAN or the ones that come 
| | with Karmic in universe?
| | 
| | Michael
| |

        
| | Hodgess, Erin wrote:

        
| | > Dear R Debian People:
| | > 
| | > I have put this on regular R help as well, but thought that I'd try here too.
| | > 
| | > I updated to R-2.10.0 on Ubuntu Karmic Koala via apt-get update, apt-get install.
| | > 
| | > Then I had a problem that said that I need MASS <= R-2.9.2.  Fair enough.  Uwe Ligges was kind enough to point out that I needed to use 
| | >> update.packges(checkBuilt=TRUE)
| | > 
| | > So I did.
| | > 
| | > Now the menu on Rcmdr does not appear.
| | > 
| | > Just as an experiment, I downloaded the R-2.10.0.tar.gz file and installed via ./configure, make, etc. and all is well there.
| | > 
| | > Any help would be much appreciated.
| | > 
| | > Thanks,
| | > Sincerely,
| | > Erin
| | > 
| | > 
| | > Erin M. Hodgess, PhD
| | > Associate Professor
| | > Department of Computer and Mathematical Sciences
| | > University of Houston - Downtown
| | > mailto: hodgesse at uhd.edu
| | > 
| | > 
| | > 	[[alternative HTML version deleted]]
| | > 
| | > _______________________________________________
| | > R-SIG-Debian mailing list
| | > R-SIG-Debian at r-project.org
| | > https://stat.ethz.ch/mailman/listinfo/r-sig-debian
| | 
| | -- 
| | Dr. Michael A. Rutter
| | School of Science
| | Penn State Erie, The Behrend College
| | Station Road
| | Erie, PA 16563
| | http://math.bd.psu.edu/faculty/rutter
| | 
| | 
| | 	[[alternative HTML version deleted]]
| | 
| | _______________________________________________
| | R-SIG-Debian mailing list
| | R-SIG-Debian at r-project.org
| | https://stat.ethz.ch/mailman/listinfo/r-sig-debian
| 
| -- 
| Three out of two people have difficulties with fractions.
|

  
    

      
      
    

  


  


      

    

    
5 days later

    

      
      

        


  

        

      denis brion
    

    

      
      #
    

  


  

      
I do not know whether this remark might be confusing, but giving a value to R_LIBS (ie something like that :
R_LIBS=/usr/local/lib/R/library:/usr/lib/R/library /usr/bin/R --vanilla #a
or
R_LIBS=/usr/lib/R/library:/usr/local/lib/R/library /usr/local/bin/R --vanilla #b
might swap the libraries of two Rs :
in the #a case, the standard R would have access to libraries for a tested R -put in /usr/local-
 and , in the case #b the tested R -compiled - would have access to libraries in an "official" place)
might give better control on the order libraries are accessed (else, ordinary users could not test new packages/libraries, in order to ignore them or recommand to their sys-admins.).

--- En date de?: Mar 24.11.09, Dirk Eddelbuettel <edd at debian.org> a ?crit?: