From jwiley.psych at gmail.com  Sun May 13 21:16:13 2012
From: jwiley.psych at gmail.com (Joshua Wiley)
Date: Sun, 13 May 2012 12:16:13 -0700
Subject: [Rd] R package dependency issues when namespace is not attached
In-Reply-To: <4FAFEBE4.5020403@statistik.tu-dortmund.de>
References: <CABFfbXuLstmkNWg3gG3cJmo=Kw33+B=8EoXK9kE9D82HA9oBLg@mail.gmail.com>
	<4FAF77DC.4040801@gmail.com>
	<4FAFEBE4.5020403@statistik.tu-dortmund.de>
Message-ID: <CANz9Z_K0UtNzqbyx1UZu5LiHJ5Tq4BVq0wtbVRFuG+ihzY08_w@mail.gmail.com>

On Sun, May 13, 2012 at 10:14 AM, Uwe Ligges
<ligges at statistik.tu-dortmund.de> wrote:
>
>
> On 13.05.2012 10:59, Duncan Murdoch wrote:
>>
>> On 12-05-13 3:15 AM, Jeroen Ooms wrote:
>>>
>>> I have always assumed that having a package in the 'Depends' field
>>> would automatically also import the namespace. However, it seems that
>>> in R 2.15, dependencies do not become available until the package is
>>> actually attached to the searchpath. Is this intended behavior?
>>>
>>> The problem appears as follows: Suppose there is a package 'Child'
>>> which Depends, but does not explicitly import a package called
>>> 'Parent' and contains a function that calls out to an object in the
>>> namespace of 'Parent'. When this function is called without attaching
>>> 'Child' to the search path, the function in 'Parent' cannot be found.
>>>
>>> Here an example from the manual of the bigdata package, but the
>>> problem is very widespread:
>>>
>>> x = matrix(rnorm(50*80),50,80)
>>> beta = c(3,2,1.5,rep(0,77))
>>> y = rnorm(50) + x%*%beta
>>> z1 = bigdata::lasso.stars(x,y)
>>>
>>> The example fails because lasso.stars depends on 'glmnet' which is not
>>> loaded until bigdata is attached. The only way to be able to call
>>> lasso.stars is to actually attach the bigdata package:
>>>
>>> library(bigdata)
>>> z1 = bigdata::lasso.stars(x,y)
>>>
>>> Now to further complicate things, it seems that this problem is
>>> inherited to any 'grandchild' package that imports, in this case, the
>>> lasso.stars function. I have a hard time finding a good example but I
>>> am sure they are out there.
>>>
>>> Is this a bug? I know that it can be avoided by asking package authors
>>> to use Imports instead of Depends, but in practice the majority of the
>>> packages on CRAN still use Depends. It seems like the problem is
>>> easily fixed if R would automatically import the namespace of any
>>> Depends packages into to the child package namespace?
>>
>>
>> Not sure if it's a bug, but the correct solution in bigdata is to import
>> the glmnet function in its NAMESPACE. Then the namespace that gets
>> loaded when you type bigdata::lasso.stars will be able to see the glmnet
>> function.
>>
>> Perhaps Depends in the DESCRIPTION file should do the import
>> automatically, but it will be faster to import just one function than
>> everything from a package that has a lot of exports. So maybe it's a bug
>> because we don't do that, but I think there would be complaints if we did.
>>
>> On the other hand, if bigdata::lasso.stars loaded glmnet onto the search
>> path, I think that would be a bug. The search path belongs to the user,
>> not to R, and the user might have used the :: notation to avoid messing
>> with it.
>
>
> I do not see any problem in R. If someone is going to import a Namespace, he
> or she has to do that via import directives in the NAMESPACE file. If
> someone is going to have a package on the search path, he or she has to
> require() it. The DESCRIPTION file is used to derive the dependency
> structures among packages for installation order, check order etc.

So should package authors both list a package in the depends of
DESCRIPTION and explicitly import what is needed so if someone else
uses their code without loading the package, everything needed is
available?

>
> Best,
> Uwe
>
>
>
>
>
>> Duncan Murdoch
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



-- 
Joshua Wiley
Ph.D. Student, Health Psychology
Programmer Analyst II, Statistical Consulting Group
University of California, Los Angeles
https://joshuawiley.com/



[Rd] R package dependency issues when namespace is not attached
Joshua Wiley