From mtmorgan at fhcrc.org  Wed May  8 19:52:06 2013
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Wed, 08 May 2013 10:52:06 -0700
Subject: [Rd] Dependencies of Imports not attached?
In-Reply-To: <71CEDD11-1D4C-40BE-A106-E2D2933EAC75@r-project.org>
References: <CAJoaRhbvZuNOezQr9-RjFzJ1O1s0+xy442wFvDsZVK=C9jXGrA@mail.gmail.com>
	<71CEDD11-1D4C-40BE-A106-E2D2933EAC75@r-project.org>
Message-ID: <518A90C6.1090501@fhcrc.org>

On 05/08/2013 10:25 AM, Simon Urbanek wrote:
>
> On May 7, 2013, at 11:35 PM, Peter Meilstrup wrote:
>
>> Encountered an error in scripting, which can be reproduced using Rscript as
>> follows:
>>
>> $ Rscript -e "library(httr); handle('http://cran.r-project.org')"
>>
>> Error in getCurlHandle(cookiefile = cookie_path, .defaults = list()) :
>>   could not find function "getClass"
>> Calls: handle -> getCurlHandle
>>
>> or by starting R without the methods package attached:
>>
>> $ R_DEFAULT_PACKAGES=base R
>> [snip]
>>> library(httr)
>>> handle('http://cran.fhcrc.org/')
>> Error in getCurlHandle(cookiefile = cookie_path, .defaults = list()) :
>>   could not find function "getClass"
>>
>> As far as I can tell the error occurs when getCurlHandle .Calls a C
>> function which then calls SET_CLASS, which (I guess) requires
>> methods::setClass to be in the search path.
>>
>> Now 'httr' Imports 'RCurl' which Depends on 'methods'. So I think
>> `library(httr)` should end up attaching 'methods' to the search path, but
>> it seems 'methods' is just imported to RCurl's namespace.
>>
>> I think this is a problem since the Depends line is indicating that
>> 'methods' must be attached for RCurl to work, whether or not RCurl itself
>> is being attached.
>>
>
> For the record, I see the same problem with other packages that use S4 - very often it trips packages that don't use S4 but import a package that does. The analysis is correct - if a package B just imports a function from another package A which in turn relies on something in Depends, it breaks, because A is not on the search path and thus A doesn't have access to the dependencies it needs. I don't know that was the intended design. I see two way to fix this
> 1) make sure Depends: are always put on the search path even if the package is not attached
> 2) automatically generate imports for all packages in Depends:
>
> The main problem is that B is helpless - only a change in A can make it work. Fix for A is to explicitly add import(methods) even though it's already in Depends:. Note that R CMD check doesn't detect this.

As described, this is a 'package maintainer' problem -- fix package A. Also, 
this isn't unique to methods, other packages routinely Depend: on something that 
should instead be Import:'ed.

But I think Peter's case is different, because the C implementations of

     SEXP R_do_MAKE_CLASS(const char *what);
     SEXP R_getClassDef  (const char *what);

need to be called from inside the package environment, but there is no way to 
pass the package environment through the interface above.

Maybe the partial patch (attached) points to a solution? It changes the 
interface (though would only break a couple of Bioconductor packages in a minor 
way) (I think there's a missing PROTECT in there too.)


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


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[Rd] Dependencies of Imports not attached?
Martin Morgan