R devel - Nov 2012 - Correct use of Depends, Imports and ::

Dear R developers,

Taking advantage of the yesterday discussion about the use of 
Depends/Import/Suggests/Enhances, I would like to add a related question.

Let's assume, in the DESCRIPTION file of my package foo0, I have:

Depends: foo1
Imports: foo2

while in the NAMESPACE file of my package I have

importFrom("foo2", f2)


and within my package I use the following two external functions:

f1, from package foo1
f2, from package foo2


If I want to use the two previous functions within a function of my 
package foo0, is it correct to call them as follow ( assuming 'x' is the
only argument of 'f1' and 'f2'):

f1(x)
foo2::f2(x)

OR should I use

foo1::f1(x)
f2(x)

OR

f1(x)
f2(x)

OR

something else (the correct way of doing it in R) ?



Finally, can I use the following call in the body of a function of my 
package foo0:

foo3::f3(x)

without declaring the package 'foo3' in the Imports section of my 
DESCRIPTION file ?


Thanks in advance for your help,


Mauricio Zambrano-Bigiarini

-- 
================================================Water Resources Unit
Institute for Environment and Sustainability (IES)
Joint Research Centre (JRC), European Commission
TP 261, Via Enrico Fermi 2749, 21027 Ispra (VA), IT
webinfo    : http://floods.jrc.ec.europa.eu/
================================================DISCLAIMER:\ "The views
expressed are purely those of th...{{dropped:11}}

On Nov 7, 2012, at 4:04 AM, Mauricio Zambrano-Bigiarini wrote:
> Dear R developers,
> 
> Taking advantage of the yesterday discussion about the use of
Depends/Import/Suggests/Enhances, I would like to add a related question.
> 
> Let's assume, in the DESCRIPTION file of my package foo0, I have:
> 
> Depends: foo1
> Imports: foo2
> 
> while in the NAMESPACE file of my package I have
> 
> importFrom("foo2", f2)
> 
> 
> and within my package I use the following two external functions:
> 
> f1, from package foo1
> f2, from package foo2
> 
> 
> If I want to use the two previous functions within a function of my package
foo0, is it correct to call them as follow ( assuming 'x' is the only
argument of 'f1' and 'f2'):
> 
> f1(x)
> foo2::f2(x)
> 
> OR should I use
> 
> foo1::f1(x)
> f2(x)
> 
> OR
> 
> f1(x)
> f2(x)
> 
Yes, this one. You have imported f2 so the whole point of that is that it will
be inserted as "f2" into your imports environment, so you want to use
it that way. When you use foo2:: you are skipping over imports and addressing
the namespace of foo2 directly which sort of defeats the purpose (and is
slower).

As for f1, you have attached the package so it is available. I would not use
foo1:: for the same reason as above, but there is a risk that it may get
clobbered since the call will go through the search path so you may not get f1
from foo1 necessarily - this may or may not be a good thing depending on your
intentions. You could import it via import(foo1) to make sure you don't need
to go through the search path - that's what I would do if I don't intend
overrides. (Whether you want to use Depends or Imports in that case is related
to what you intend for the user to see as I was saying in my last comment - if I
expect users to use foo1 as well, I would use Depends, otherwise Imports is good
enough.)

> OR
> 
> something else (the correct way of doing it in R) ?
> 
> 
> 
> Finally, can I use the following call in the body of a function of my
package foo0:
> 
> foo3::f3(x)
> 
> without declaring the package 'foo3' in the Imports section of my
DESCRIPTION file ?
> 
No, it has to be at least in Enhances or Suggests (see R-exts 1.1.1).

Cheers,
Simon

> 
> Thanks in advance for your help,
> 
> 
> Mauricio Zambrano-Bigiarini
> 
> -- 
> ================================================> Water Resources Unit
> Institute for Environment and Sustainability (IES)
> Joint Research Centre (JRC), European Commission
> TP 261, Via Enrico Fermi 2749, 21027 Ispra (VA), IT
> webinfo    : http://floods.jrc.ec.europa.eu/
> ================================================> DISCLAIMER:\ "The
views expressed are purely those of th...{{dropped:11}}
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
>

On 07/11/2012 20:26, Yanming Di wrote:
> Hi all,
>
> In a package I maintain, I use the "dqrls" from the base package
to fit
> regression models. However, I was informed that directly calling
> functions from the base package is no longer allowed:
>
> "CRAN packages should use only the public API. Hence they should not
use
> entry points not declared as API in installed headers nor .Internal()
> nor .Call() etc calls to base packages. Such usages can cause packages
> to break at any time, even in patched versions of R."
And dqrls is no longer available via .Fortran in R-devel.
> Prof. Ripley suggested that one can replace such calls with lm.wfit,
> which will work.
>
> However, in my package, the call will need to be implemented hundreds of
> thousands times. Using lm.wfit is much slower. I am wondering whether
> there is alternative ways that are more efficient. I can program in C if
> needed.
If the licence of your package allows it, you can copy the Fortran code 
into your package and write your own interface via .Fortran, .C or .Call.

The .Fortran interface is itself quite costly, especially in R < 2.15.1: 
in some cases lm.wfit is actually faster as it uses .Call.
>
> Many thanks.
>
> Best regards,
> Yanming
>
> ______________________________________________
> 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