From ligges at statistik.tu-dortmund.de  Sun May 13 19:14:12 2012
From: ligges at statistik.tu-dortmund.de (Uwe Ligges)
Date: Sun, 13 May 2012 19:14:12 +0200
Subject: [Rd] R package dependency issues when namespace is not attached
In-Reply-To: <4FAF77DC.4040801@gmail.com>
References: <CABFfbXuLstmkNWg3gG3cJmo=Kw33+B=8EoXK9kE9D82HA9oBLg@mail.gmail.com>
	<4FAF77DC.4040801@gmail.com>
Message-ID: <4FAFEBE4.5020403@statistik.tu-dortmund.de>



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.

Best,
Uwe




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



[Rd] R package dependency issues when namespace is not attached
Uwe Ligges