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. > library(Matrix) > sm <- as(as(Matrix(diag(5) + 1), "dsyMatrix"), "dspMatrix") > library(SparseM) [1] "SparseM library loaded" > chol(sm) Error in chol(sm) : no applicable method for "chol" > Matrix::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 You might want to discuss this with the SparseM package maintainers; perhaps they don't really need to define their own generic. Duncan Murdoch> > 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 >> > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel
Both are contributed packages. The R-bugs repository is for bugs in R, not for contributed packages, as clearly stated in the R FAQ. Finally, check carefully whether the bug is with R, or a contributed package. Bug reports on contributed packages should be sent first to the package maintainer, and only submitted to the R-bugs repository by package maintainers, mentioning the package in the subject line. Please contact the maintainers. (It looks to me as if the problem is in SparseM, so you could try loading it first.) On Mon, 20 Feb 2006, 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. > > 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 >> > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > >-- 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