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Having problems with quantreg

4 messages · mark engle, Dirk Eddelbuettel

Original
mark engle
# 
Hi All,
     I'm still having significantly difficulty getting the quantreg library 
running in R.  I'm running R on MEPIS using the debs created by Dirk 
Eddelbuettel and placed in apt testing.  When I try to install quantreg using 
the install.packages() function it fails with:  /usr/bin/ld: cannot find 
-lblas-3

Dirk was nice enough to send me a .deb for quantreg which installs without 
error.  However, when I try to run the rq command after entering 
library(quantreg), I get: Error: Object "rq" not found

I've tried reinstalling atlas3-base (as Douglas Bates suggested), every R 
package on my machine and ripping out every config file I can find and 
re-installing to no avail.    I am a true beginner at R and could certainly 
be doing something or just be missing a package.  If anyone has anymore 
ideas, I'd love to hear them.  Thanks for the help.
-Mark

engle at unr dot nevada dot edu
Dirk Eddelbuettel
#
On 21 February 2005 at 22:42, mark engle wrote:
| Hi All,
|      I'm still having significantly difficulty getting the quantreg library 
| running in R.  I'm running R on MEPIS using the debs created by Dirk 
| Eddelbuettel and placed in apt testing.  When I try to install quantreg using 
| the install.packages() function it fails with:  /usr/bin/ld: cannot find 
| -lblas-3
| 
| Dirk was nice enough to send me a .deb for quantreg which installs without 
| error.  However, when I try to run the rq command after entering 
| library(quantreg), I get: Error: Object "rq" not found
| 
| I've tried reinstalling atlas3-base (as Douglas Bates suggested), every R 
| package on my machine and ripping out every config file I can find and 
| re-installing to no avail.    I am a true beginner at R and could certainly 
| be doing something or just be missing a package.  If anyone has anymore 
| ideas, I'd love to hear them.  Thanks for the help.

i)   I know little about MEPIS, and in particular R on MEPIS. Take everything
     with a grain of salt, and if in doubt, test on a proper Debian machine.
     Try to find one somewhere at nevada.edu. It will easier for us to get it
     to work there -- and let's then try to apply what we learned on your
     MEPIS box.

ii)  The (autogenerated) quantreg package I sent you has Depends as follows:

edd@chibud:~> dpkg -f src/progs/perl/cran2deb/builds/r-cran-quantreg_3.50-0.r2d.1_i386.deb
Package: r-cran-quantreg
Version: 3.50-0.r2d.1
Section: math
Priority: optional
Architecture: i386
Depends: atlas3-base | refblas3 | libblas.so.3, libc6 (>= 2.3.2.ds1-4), libg2c0(>= 1:3.3.4-1), libgcc1 (>= 1:3.4.1-3), r-base-core
Installed-Size: 848
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Source: quantreg
Description: GNU R package "Quantile Regression"
 Quantile  regression and related methods.
 .
 Author(s): Roger Koenker <rkoenker@uiuc.edu>
 Initial R port from Splus by Brian Ripley <ripley@stats.ox.ac.uk>
 Date:
 .
 URL: http://www.econ.uiuc.edu/~roger/research/rq/rq.html

 
     Notice how it says "atlas3-base | refblas3 | libblas.so.3"  What you
     need is a concrete package that provides the virtual package
     libblas.so.3.

     You tried atlas3-base, and it didn't work.  The next thing to try would
     be refblas3. Install that and see what it does.

     Afterwards there are the others:

edd@chibud:~> apt-cache showpkg libblas.so.3
Package: libblas.so.3
Versions:

Reverse Depends:
  r-cran-matrix,libblas.so.3
  r-cran-rscalapack,libblas.so.3
[...]
Dependencies:
Provides:
Reverse Provides:
refblas3 1.2-6
atlas3-sse2 3.6.0-19
atlas3-sse 3.6.0-19
atlas3-base 3.6.0-19
atlas3-3dnow 3.6.0-19
edd@chibud:~>                     

     Anyone of those after the "Reverse Provides" will do, but the
     hardware-optimised ones (atlas3-sse2, -sse2, -3dnow) only makes
     sense on the matching hardware.

Hope this helps, Dirk


| -Mark
| 
| engle at unr dot nevada dot edu
| 
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| R-SIG-Debian mailing list
| R-SIG-Debian@r-project.org
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mark engle
# 
Thanks for all of the help.  I had already installed refblas3.  I installed 
atlas3-sse, which didn't seem to change anything.  I then added 
atlas3-base-dev (seems kind of obvious now) and the quantreg package compiled 
from source and commands from the package are now recognized.  I'm going to 
give it a quick run around the block but I think that will solve everything 
for me.  Thanks again.
-Mark
On Tuesday 22 February 2005 5:16, Dirk Eddelbuettel wrote:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Dirk Eddelbuettel
    

    

      
      #
    

  


  

      
On 22 February 2005 at 15:01, mark engle wrote:

        
| Thanks for all of the help.  I had already installed refblas3.  I installed 
| atlas3-sse, which didn't seem to change anything.  I then added 
| atlas3-base-dev (seems kind of obvious now) and the quantreg package compiled 
| from source and commands from the package are now recognized.  I'm going to 
| give it a quick run around the block but I think that will solve everything 
| for me.  Thanks again.

So I suspect you never had the r-base-dev package installed which would have
lead you to having a -dev package providing blas-3 development headers and
libs.  

Hm, Doug and I should have checked that first ...

Anyway, glad to hear you have it working now.

Regards,  Dirk