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
______________________________________________
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.
