From patrick.giraudoux at univ-fcomte.fr  Sun Mar 18 20:05:02 2012
From: patrick.giraudoux at univ-fcomte.fr (Patrick Giraudoux)
Date: Sun, 18 Mar 2012 20:05:02 +0100
Subject: [Rd] Namespace dependency not required
In-Reply-To: <4F6629DA.2070700@statistik.tu-dortmund.de>
References: <4F65B73B.8010809@univ-fcomte.fr>
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	<4F6629DA.2070700@statistik.tu-dortmund.de>
Message-ID: <4F6631DE.7020608@univ-fcomte.fr>

Le 18/03/2012 19:30, Uwe Ligges a ?crit :
>
>
> On 18.03.2012 19:27, Patrick Giraudoux wrote:
>> Le 18/03/2012 18:02, Uwe Ligges a ?crit :
>>>
>>>
>>> On 18.03.2012 16:08, Patrick Giraudoux wrote:
>>>> Le 18/03/2012 14:57, Uwe Ligges a ?crit :
>>>>>
>>>>>
>>>>> On 18.03.2012 11:21, Patrick Giraudoux wrote:
>>>>>> Hi,
>>>>>>
>>>>>> I am working at adding namespace to my packages, carefully
>>>>>> following the
>>>>>> doc "Writing R extensions" and some threads on the web. However I
>>>>>> cannot
>>>>>> find clear explanation about how to best deal with the import or
>>>>>> importFrom functions in the name space. To make it short:
>>>>>>
>>>>>> To declare dependencies in the description file either after 
>>>>>> Depends:
>>>>>> (packages including functions that are called from a package 
>>>>>> function)
>>>>>> or after Suggests: (packages that are called eg from the 
>>>>>> doucmentation
>>>>>> examples), works well. In this case one does not need to declare
>>>>>> import
>>>>>> in the namespace file.
>>>>>>
>>>>>> However, declaring dependencies sometimes for using only one
>>>>>> function in
>>>>>> a given package looks a bit over the top, and I though I could use
>>>>>> importFrom in the namespace to deal with that. So removing the
>>>>>> corresponding declaration in Depends (description file) and 
>>>>>> declaring
>>>>>> eg importFrom(splancs, inout) in the namespace always led to:
>>>>>>
>>>>>> * checking package dependencies ... ERROR
>>>>>> Namespace dependency not required: 'splancs'
>>>>>>
>>>>>> Same thing with import(sp). I have the same trouble if I do not 
>>>>>> remove
>>>>>> the declarations in Depends.
>>>>>>
>>>>>> So, I can hardly follow the meaning of the "Writing R extension" 
>>>>>> doc:
>>>>>>
>>>>>> Packages implicitly import the base namespace. Variables exported 
>>>>>> from
>>>>>> other packages with namespaces need to be imported explicitly using
>>>>>> the
>>>>>> directives |import| and |importFrom|. The |import| directive
>>>>>> imports all
>>>>>> exported variables from the specified package(s). Thus the 
>>>>>> directives
>>>>>>
>>>>>> import(foo, bar)
>>>>>>
>>>>>> specifies that all exported variables in the packages *foo* and 
>>>>>> *bar*
>>>>>> are to be imported. If only some of the exported variables from a
>>>>>> package are needed, then they can be imported using |importFrom|. 
>>>>>> The
>>>>>> directive
>>>>>>
>>>>>> importFrom(foo, f, g)
>>>>>>
>>>>>> specifies that the exported variables |f| and |g| of the package 
>>>>>> *foo*
>>>>>> are to be imported.
>>>>>>
>>>>>> Can anybody tell us the conditions for which import and importFrom
>>>>>> commands should be used in the NAMESPACE rather than in the Depends
>>>>>> and
>>>>>> Suggests declarations of the description file, and the conditions of
>>>>>> their applicability (without error message... eg with a working
>>>>>> example) ?
>>>>>
>>>>> If you import from another namespace (which is the recommended way
>>>>> rather than just relying on search order), do not forget to 
>>>>> declare it
>>>>> as "Imports" in your DESCRIPTION file. Your package depends on the
>>>>> other one: It could not be loaded without having the other one
>>>>> installed now.
>>>>>
>>>>> Uwe Ligges
>>>>>
>>>>
>>>> OK. got it (more or less).
>>>>
>>>> With this in the description file:
>>>>
>>>> Depends: boot (>= 1.3-4), nlme(>= 3.1-64), rgdal (>= 0.7-8), sp (>=
>>>> 0.9-97), spdep (>= 0.5-43), splancs (>= 2.01-31)
>>>>
>>>> importFrom(splancs, inout) is accepted in the NAMESPACE file and I 
>>>> have
>>>> no error message with rcmd check.
>>>>
>>>> Irr works also with:
>>>>
>>>> Depends: boot (>= 1.3-4), nlme(>= 3.1-64), rgdal (>= 0.7-8), sp (>=
>>>> 0.9-97), spdep (>= 0.5-43)
>>>> Imports: splancs (>= 2.01-31)
>>>>
>>>> Practically, I a am safe (thanks a lot), but I am however still hungry
>>>> to learn a bit more. I hardly understand what R does when reading the
>>>> suggests and imports in the DESCRIPTION file compared to what it does
>>>> reading the NAMESPACE (my mistake was to believe that one was a
>>>> substitute for the other). From a practical point of view, why is it
>>>> important to use import or importFrom in the NAMESPACE when everything
>>>> looks like working well when declarations are done in the DESCRIPTION
>>>> file only (eg in depends or imports)? It is not crystal clear to me 
>>>> even
>>>> reading carefully "Writing R extension". DESCRIPTION file is used 
>>>> to get
>>>> the "list of packages that will be attached (...) before the current
>>>> package" (indeed, now, I no longer needs to use 'require' within my
>>>> package functions). In simple words, what may add the NAMESPACE to
>>>> that ?
>>>>
>>>> Apologize to be so poorly aware (= so much stupid) about the role of
>>>> each of those declaration spaces.
>>>
>>> Please read some literature about NAMESPACES, e.g. documentation in
>>> Writing R Extensions plus Luke Tierney's articles in R News.
>>
>> ok. Will do it with Luke Tierney's articles. I read Writing R extensions
>> already and also S programming (Venables and Ripley), but indeed should
>> come down to more basic text for dudes :-) .
>
> S Programming is excellent, but it was written before Namespaces were 
> introduced to R.
>
> Uwe Ligges
>
>
>
>
>>
>> Best,
>>
>> Patrick
>>
>>
>>>
>>> A NAMESPACE import imports functionality of another namespace into
>>> your own namespace and hence avoids problems caused by name clashes.
>>> The DESCRIPTION file is required to derive dependency structure of
>>> packages, i.e. derive which package has to be *installed* first etc.
>>>
>>> Uwe Ligges
>>>
>>
>


Great ! Luke Tierney's article in R news is particularly clear (to me) 
with nice examples on how namespace avoids variable shadowing. I give 
the link here for any user/developper who may follow the thread on this 
issue: http://journal.r-project.org/archive.html Volume 3/1 June 2003, 
Name Space Management for R by Luke Tierney.

Thanks Uwe for the hint.

Best,

Patrick



[Rd] Namespace dependency not required
Patrick Giraudoux