[Rd] particulars of importing/loading libraries

[Sklyar, Oleg (London)]

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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