particulars of importing/loading libraries

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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