Matrix / SparseM conflict (PR#8618)

Full_Name: David Pleydell
Version: 2.2.1
OS: Debian Etch
Submission from: (NULL) (193.55.70.206)


There appears to be a conflict between the chol functions from the Matrix and
the SparseM packages. chol() can only be applied to a matrix of class dspMatrix
if SparseM is not in the path.

with gratitude
David

library(Matrix)
sm <- as(as(Matrix(diag(5) + 1), "dsyMatrix"), "dspMatrix")
chol(sm)

5 x 5 Matrix of class "pCholesky"
     [,1]      [,2]      [,3]      [,4]      [,5]     
[1,] 1.4142136 0.7071068 0.7071068 0.7071068 0.7071068
[2,]         . 1.2247449 0.4082483 0.4082483 0.4082483
[3,]         .         . 1.1547005 0.2886751 0.2886751
[4,]         .         .         . 1.1180340 0.2236068
[5,]         .         .         .         . 1.0954451

library(SparseM)

[1] "SparseM library loaded"

chol(sm)

Error in chol(sm) : no applicable method for "chol"

detach("package:SparseM")
chol(sm)

5 x 5 Matrix of class "pCholesky"
     [,1]      [,2]      [,3]      [,4]      [,5]     
[1,] 1.4142136 0.7071068 0.7071068 0.7071068 0.7071068
[2,]         . 1.2247449 0.4082483 0.4082483 0.4082483
[3,]         .         . 1.1547005 0.2886751 0.2886751
[4,]         .         .         . 1.1180340 0.2236068
[5,]         .         .         .         . 1.0954451

On 2/20/2006 8:54 AM, dpleydel at univ-fcomte.fr wrote:

Full_Name: David Pleydell
Version: 2.2.1
OS: Debian Etch
Submission from: (NULL) (193.55.70.206)


There appears to be a conflict between the chol functions from the Matrix and
the SparseM packages. chol() can only be applied to a matrix of class dspMatrix
if SparseM is not in the path.

This isn't a bug, it's simply that both Matrix and SparseM define a
generic for chol (though Matrix actually gets it by converting the
function in base).

If you want access to the version in Matrix after attaching SparseM
ahead of it in the search path, use Matrix::chol.

On Mon, 20 Feb 2006, Duncan Murdoch wrote:

On 2/20/2006 8:54 AM, dpleydel at univ-fcomte.fr wrote:

Full_Name: David Pleydell
Version: 2.2.1
OS: Debian Etch
Submission from: (NULL) (193.55.70.206)


There appears to be a conflict between the chol functions from  
the Matrix and
the SparseM packages. chol() can only be applied to a matrix of  
class dspMatrix
if SparseM is not in the path.

This isn't a bug, it's simply that both Matrix and SparseM define a
generic for chol (though Matrix actually gets it by converting the
function in base).

The problem appears to be that SparseM first redefines chol as an  
S3 generic and then defines S4 methods on it.  As no new S3 methods  
are then defined the S3 step would seem unnecessary, but it is used  
to allow the package to define S4 methods on a different signature  
from R's chol().
(That seems to me to be asking for trouble.)

Only the package maintainer of SparseM can do anything about this.

Beyond, that I guess it is a consequence of namespaces that Matrix  
defines methods via a derived generic on base::chol and not on the  
generic chol in SparseM.  That needs further thought by someone  
(JMC?) who understands the S4 internals.

If you want access to the version in Matrix after attaching SparseM
ahead of it in the search path, use Matrix::chol.

But the whole point of generic functions is to allow one to write  
generic code.

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595