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
[...]
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