On 23.11.2011 16:38, Gábor Csárdi wrote:
Just for the records, the solution was to make the matrix 'dgCmatrix"
instead of 'dsCmatrix', 'dgCmatrix' works and 'dsCmatrix' does not. I
suspect that this has to do something with the S4 class hierarchy in
Matrix, but I am not sure.
This is a quite ugly workaround, since it depends on some internal
Matrix features, so I might end up just importing Matrix, as many of
you suggested in the first place....
However, I agree with Gabor Grotherdieck that the issue is still
there, in general.
Another example would be (optionally) using the 'snow' (or now
'parallel') package. I would like to add optional parallel processing
to some of my functions in a package, without actually requiring the
installation of snow/parallel.
Errr, parallel as a base package is *always* installed for R >= 2.14.0.
If snow is there and the user wants to
use it, then it is used, otherwise not.
Actually, 'snow' works similarly. It (optionally) calls function from
the Rmpi package, but Rmpi is only suggested, there is no hard
dependency. This seems to work well for snow, but in my case I the S4
features in Matrix interfere.
Well the is an important difference here: Rmpi does not produce name
clashes and its functionality is found when it is simply attached to the
search path in the case of snow. The problem with Matrix is that you
import from base and hence base names are found before Matrix names.
Hence require()ing Matrix as a suggest and calling directly
Matrix::rowSums explicitly and so on should work. And exactly this is
what Namespaces are made for: deal appropriately with name clashes by
importing into the own namespace.
Best,
Uwe Ligges
Gabor
On Tue, Nov 22, 2011 at 8:09 PM, Gábor Csárdi<csa...@rmki.kfki.hu> wrote:
Dear Martin,
thanks a lot, this all makes sense and looks great. I suspected some
S4 trickery and totally forgot that the base package is imported
automatically.
Unfortunately I still get
Error in callGeneric() :
'callGeneric' must be called from a generic function or method
for my real function, but it works fine for the toy f() function, so I
think I can sort this out from here.
Best Regards,
Gabor
On Tue, Nov 22, 2011 at 6:57 PM, Martin Morgan<mtmor...@fhcrc.org> wrote:
On 11/22/2011 03:06 PM, Gábor Csárdi wrote:
On Tue, Nov 22, 2011 at 4:27 PM, Martin Morgan<mtmor...@fhcrc.org> wrote:
[...]
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...?
Not just loading, installing a package has a cost, too. Dependencies
are bad, they might make my package fail, and I have no control over
them. It's not just 'Matrix', I have this issue with other packages as
well.
Anyway, 'Imports: Matrix' is just a workaround I think. Or is the
example in my initial mail expected to fail? Why is that? Why can I
call some functions from 'Matrix' that way and why can't I call
others?
I'm more into black-and-white -- it either needs Matrix or not;
apparently
it does.
It's a matter of opinion, I guess. I find it very annoying when I need
to install a bunch of packages from which I don't use any code, just
because some tiny bit of a package I need uses them. I would like to
spare my users from this.
[...]
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?
Another poster suggested this, that's why I tried. It is clear that I
should not call it directly. All I want to do is having a function
like this:
f<- function() {
if (require(Matrix)) {
res<- sparseMatrix(dims=c(5, 5), i=1:5, j=1:5, x=1:5)
} else {
res<- diag(1:5)
}
y<- rowSums(res)
res / y
}
Setting the subjective bit, about depending or not, aside, is there
really no solution for this? The code in the manual page examples work
fine without importing the package and just loading it if needed and
available. Why doesn't the code within the package?
If I create a package that does not Import: Matrix (btw, Matrix is
distributed with all R), with only a function f, and with exports(f) in
NAMESPACE, I get
library(pkgA)
f()
Loading required package: Matrix
Loading required package: lattice
Attaching package: 'Matrix'
The following object(s) are masked from 'package:base':
det
Error in rowSums(res) : 'x' must be an array of at least two dimensions
This is because (a) Matrix is attached to the user search path but (b)
because f is defined in the NAMESPACE of pkgA, rowSums is looked for first
in the pkgA NAMESPACE, and in then in the search of the package (which
includes base) and then in the user search path. It is found in base, and
the search ends there.
If I modify f to use y<- Matrix::rowSums(res) I get
f()
Loading required package: Matrix
Loading required package: lattice
Attaching package: 'Matrix'
The following object(s) are masked from 'package:base':
det
5 x 5 sparse Matrix of class "dgCMatrix"
[1,] 1 . . . .
[2,] . 1 . . .
[3,] . . 1 . .
[4,] . . . 1 .
[5,] . . . . 1
I start off with the correct rowSums, and continue from there.
Martin
Thanks for the patience,
Gabor
Martin
[...]
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
--
Gabor Csardi<csa...@rmki.kfki.hu> MTA KFKI RMKI
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