On 11/22/2011 01:16 PM, Gábor Csárdi wrote:
Hi Josh,
On Tue, Nov 22, 2011 at 3:31 PM, Joshua Wiley<jwiley.ps...@gmail.com> wrote:
Hi Gábor,
You could import rowSums. This will not fully attach Matrix. I am
not sure there is a really good solution for what you want to do. To
fully use and validate your package, Matrix appears to be required.
This is different from simply, for example, enhancing the Matrix
package.
importing rowSums() from NAMESPACE requires having Matrix in the
'Depends:' line, I think. I would like to avoid that, if possible.
No need to Depend:. Use
Imports: Matrix
plus in the NAMESPACE file
importFrom(Matrix, rowSums)
Why do you not want to do this? Matrix is available for everyone,
Imports: doesn't influence the package search path. There is a cost
associated with loading the library in the first place, but...?
Sure, to validate my package it is required. That is fine. For "fully"
using it might be required, but most users don't fully use a package,
they just use 1-20-50% of the functionality, depending on the size of
the package. My package does not depend on Matrix, except in less than
1% of its (quite many) functions.
I'm more into black-and-white -- it either needs Matrix or not;
apparently it does.
You could just write the functions assuming matrix is there, make sure
the examples are marked don't run, and tell users if they want to use
them, they need to load Matrix first. I do this with OpenMx in my
package.
Hmmm, this is close to what I want to do. Actually my functions work,
even if Matrix is not there, but they work better with Matrix. The
problem is that if I do this, then I get the error I've shown in my
initial email. I.e. Matrix is there, it is loaded, but the rowSums()
generic is not called for some reasons.
In another message you mention
> Matrix:::rowSums(W)
Error in callGeneric() :
'callGeneric' must be called from a generic function or method
but something else is going on -- you don't get to call methods
directly; you're getting Matrix::rowSums (it's exported, so no need for
a :::, see getNamespaceExports("Matrix")). Maybe traceback() after the
error would be insightful?
Martin
Thanks again,
Gabor
Cheers,
Josh
On Tue, Nov 22, 2011 at 12:16 PM, Gábor Csárdi<csa...@rmki.kfki.hu> wrote:
Dear All,
in some functions of my package, I use the Matrix S4 class, as defined
in the Matrix package.
I don't want to depend on Matrix, however, because my package is
perfectly fine without Matrix, most of the functionality does not need
Matrix. Matrix is so included in the 'Suggests' line.
I load Matrix via require(), from the functions that really need it.
This mostly works fine, but I have an issue now that I cannot sort
out.
If I define a function like this in my package:
f<- function() {
require(Matrix)
res<- sparseMatrix(dims=c(5, 5), i=1:5, j=1:5, x=1:5)
y<- rowSums(res)
res / y
}
then calling it from the R prompt I get
Error in rowSums(res) : 'x' must be an array of at least two dimensions
which basically means that the rowSums() in the base package is
called, not the S4 generic in the Matrix package. Why is that?
Is there any way to work around this problem, without depending on Matrix?
I am doing this on R 2.14.0, x86_64-apple-darwin9.8.0.
Thank You, Best Regards,
Gabor
--
Gabor Csardi<csa...@rmki.kfki.hu> MTA KFKI RMKI
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Joshua Wiley
Ph.D. Student, Health Psychology
Programmer Analyst II, ATS Statistical Consulting Group
University of California, Los Angeles
https://joshuawiley.com/
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
