[Rd] particulars of importing/loading libraries

Tue Jan 13 19:23:26 CET 2009

Maybe I'm missing something (it wouldn't be the first time), but I think 
your problem is that pack2 needs a function

   .onLoad <- function(library, section) {require("pack1")}

since you actually want the functions from pack1 available, and not just 
its namespace.

( And you will need the "pack1::" in  pack1::testPosixVal only if 
testPosixVal is not exported from pack1. )

Paul

Sklyar, Oleg (London) wrote:
> I was thinking of this, but this is going to be a pain if a package
> imports 5 packs, is being imported by another one, which itself is
> imported by yet another one and the only one one would like to load
> explicitly is the last down the line. If I do not find a better solution
> this is what I probably will have to do, reexport everything. 
> 
> Dr Oleg Sklyar
> Research Technologist
> AHL / Man Investments Ltd
> +44 (0)20 7144 3107
> osklyar at maninvestments.com 
> 
>> -----Original Message-----
>> From: Martin Morgan [mailto:mtmorgan at fhcrc.org] 
>> Sent: 13 January 2009 16:31
>> To: Sklyar, Oleg (London)
>> Cc: r-devel at r-project.org
>> Subject: Re: [Rd] particulars of importing/loading libraries
>>
>> Hi Oleg --
>>
>> "Sklyar, Oleg (London)" <osklyar at maninvestments.com> writes:
>>
>>> Dear List:
>>>
>>> Sorry for posting maybe a trivial question, but I have a basic
>>> understanding problem. If I have say pack1 and pack2, two R 
>> packages,
>>> and pack2 depends on and imports pack1 fully (as in the 
>> code below), is
>>> there a way to make all the functionality of pack1 available for the
>>> global and other environments (not only for the functions 
>> called from
>>> withing pack2) by loading pack2 only? I thought if pack2 
>> depends on and
>>> imports pack1 and essentially reexports everything, one 
>> should get the
>>> full functionality simply by loading pack2. This does not 
>> seem to be the
>>> case or I am missing something trivial in my NAMESPACE/DESCRIPTION
>>> files?
>> I think that exportPattern does a simple ls() on the environment of
>> the package name space. The imported symbols are not defined in that
>> environment, but (I think) in a variable .__NAMESPACE__. and so are
>> not discovered.  Arguably, exportPattern (and friends) should be
>> smarter. Pragmatically, you need to re-export imported symbols
>> explicitly. I haven't worked this through entirely, and could be
>> wrong...
>>
>> Martin
>>
>>> If this is documented in Writing R Extensions, I would be 
>> thankful for a
>>> page number and maybe a quick fix in my example below as so 
>> far I have
>>> not been able to find a clear explanation.
>>>
>>> The problem can be illustrated by the following simple 
>> example (this is
>>> a simple code for 2 packages, pack1 and pack2; plus an example).
>>>
>>> Thank you for your replies.
>>>
>>> Dr Oleg Sklyar
>>> Research Technologist
>>> AHL / Man Investments Ltd
>>> +44 (0)20 7144 3107
>>> osklyar at maninvestments.com
>>>
>>> --- pack1: DESCRIPTION ------
>>> Package: pack1
>>> Version: 0.0.1
>>> Date: 12 Jan 2009
>>> Title: pack1 to test S3/S4 methods compatibility
>>> Author:  Oleg Sklyar
>>> Depends: R (>= 2.7.1), methods
>>> Maintainer: Oleg Sklyar <osklyar at maninvestments.com>
>>> Description: pack1
>>> LazyLoad: yes
>>> License: Proprietary
>>> URL: http://www.maninvestments.com
>>> LazyLoad: no
>>>
>>> --- pack1: NAMESPACE ------
>>> import(methods)
>>> exportPattern("^[^\\.]")
>>> exportClasses(posixTime)
>>> exportMethods(as.POSIXct)
>>>
>>> --- pack1: posix.R ------
>>> setClass("posixTime", "numeric")
>>>
>>> setGeneric("as.POSIXct")
>>> setMethod("as.POSIXct", signature(x="posixTime"),
>>>     function(x, tz) {
>>>         z = x at .Data
>>>         attr(z,"class") = c("POSIXt", "POSIXct")
>>>         attr(z,"tzone") = "UTC"
>>>         z
>>>     }
>>> )
>>>
>>> testPosixVal = new("posixTime", as.numeric(Sys.time()))
>>>
>>> --- pack2: DESCRIPTION 
>>> Package: pack2
>>> Version: 0.0.1
>>> Date: 12 Jan 2009
>>> Title: pack2 to test S3/S4 methods compatibility
>>> Author:  Oleg Sklyar
>>> Depends: R (>= 2.7.1), methods
>>> Maintainer: Oleg Sklyar <osklyar at maninvestments.com>
>>> Description: pack2
>>> LazyLoad: yes
>>> License: Proprietary
>>> URL: http://www.maninvestments.com
>>> LazyLoad: no
>>>
>>> --- pack2: NAMESPACE ------
>>> import(pack1)
>>> exportPattern("^[^\\.]")
>>>
>>> --- pack2: posix.R ------
>>> testPosix = function() {
>>>     z = as.POSIXct(testPosixVal)
>>>     print(z)
>>>     print(class(z))
>>>     z
>>> }
>>>
>>> ------ test code to run from global env, showing problems -------
>>> require(pack2)
>>>
>>> ## use as.POSIXct imported into pack2 from pack1 to do the 
>> conversion in
>>> the fun
>>> testPosix()
>>> #~ [1] "2009-01-13 15:29:50 UTC"
>>> #~ [1] "POSIXt"  "POSIXct"
>>> #~ [1] "2009-01-13 15:29:50 UTC"
>>>
>>> ## now try using it directly from the global env (pack1 was not
>>> explicitly loaded)
>>> as.POSIXct(pack1::testPosixVal)
>>> #~ Error in as.POSIXct.default(pack1::testPosixVal) : 
>>> #~  do not know how to convert 'pack1::testPosixVal' to 
>> class "POSIXlt"
>>> ## now require pack1 explicitly and try again
>>> require(pack1)
>>> as.POSIXct(pack1::testPosixVal)
>>> #~ [1] "2009-01-13 15:29:50 UTC"
>>>
>>>
>>>
>> **********************************************************************
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>> -- 
>> Martin Morgan
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>> Location: Arnold Building M2 B169
>> Phone: (206) 667-2793
>>
> 
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La version française suit le texte anglais.

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