particulars of importing/loading libraries

library(pack3)

testPosix() ## from pack2

testPosix2()

as.POSIXct(pack1::testPosixVal)

-----Original Message-----
From: Simon Urbanek [mailto:simon.urbanek at r-project.org] 
Sent: 14 January 2009 15:38
To: Sklyar, Oleg (London)
Cc: r-devel at r-project.org
Subject: Re: [Rd] particulars of importing/loading libraries


On Jan 14, 2009, at 4:24 , Sklyar, Oleg (London) wrote:

Sorry Simon, you are right. I tried to recreate a problem 

that I had  

with other packages where the packages were added to Depends but  
made a mistake. However the problem remains if I do the following.

Added: pack1 to Depends of pack2. Now I create pack3 with the  
following contents: it does not import pack1 directly, nor depends  
on it. It rather imports pack2 and depends on pack2. I then expect  
the functionality of pack1 to be available still if I only 

load pack3.


That is semantically not a reasonable requirement. pack3 cannot (and  
should not) assume anything about the internals of pack2. If 
it needs  
a function from pack1, it has to import it from pack1. If pack2 re- 
exported as.POSIXct then that would make it part of pack2's 
interface  
and then you're free to just depend on pack2.

Cheers,
S

But I
now get errors with pack3 calling the function from pack1. Does this
mean I need to import and depend on pack1 and methods explicitly in
pack3. I.e. do I have to import and depend on ALL the 

packages that  

may
be in use, even if they are imported by other that I depend on and
import:

---- pack3: DESCRIPTION -----

Package: pack3
Version: 0.0.1
Date: 12 Jan 2009
Title: pack1 to test S3/S4 methods compatibility
Author:  Oleg Sklyar
Depends: R (>= 2.7.1), pack2
Maintainer: Oleg Sklyar <osklyar at maninvestments.com>
Description: pack3
LazyLoad: yes
License: Proprietary
URL: http://www.maninvestments.com
LazyLoad: no

---- pack3: NAMESPACE ------
import(pack2)
exportPattern("^[^\\.]")

---- pack3: posix.R ------
testPosix2 = function() {
   z = as.POSIXct(testPosixVal)
   print(z)
   print(class(z))
   z
}

Note, that the above function is the same as in pack2, just a  
different
name.


*** R 2.9.0 (svn -r 46585) 

[/share/research/R-devel/20081002/lib64/R]

***

library(pack3)

Loading required package: pack2
Loading required package: pack1

as.POSIXct(pack1::testPosixVal)

[1] "2009-01-13 15:29:50 UTC"

testPosxi() ## called from pack2

[1] "2009-01-13 15:29:50 UTC"
[1] "POSIXt"  "POSIXct"
[1] "2009-01-13 15:29:50 UTC"

testPosix2() ## called from pack3

Error in as.POSIXct.default(testPosixVal) :
 do not know how to convert 'testPosixVal' to class "POSIXlt"




Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
osklyar at maninvestments.com

-----Original Message-----
From: Simon Urbanek [mailto:simon.urbanek at r-project.org]
Sent: 14 January 2009 01:51
To: Sklyar, Oleg (London)
Cc: r-devel at r-project.org
Subject: Re: [Rd] particulars of importing/loading libraries

Oleg,

On Jan 13, 2009, at 11:00 , Sklyar, Oleg (London) wrote:

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?

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).

if you bothered to use R CMD check you would find your bug right  
away:
* checking package dependencies ... ERROR
Namespace dependencies not required:
  pack1

You simply forgot to add pack1 to the Depends: line - that's
all. Once
you fix that, you'll see what happens:

library(pack2)

Loading required package: pack1

as.POSIXct(pack1::testPosixVal)

[1] "2009-01-14 01:38:08 UTC"

Cheers,
S

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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