-----Original Message-----
From: Martin Morgan [mailto:mtmor...@fhcrc.org] Sent: 13 January 2009
16:31
To: Sklyar, Oleg (London)
Cc: r-devel@r-project.org
Subject: Re: [Rd] particulars of importing/loading libraries
Hi Oleg --
"Sklyar, Oleg (London)" <oskl...@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
oskl...@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 <oskl...@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...@.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 <oskl...@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.
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