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Sklyar, Oleg (London)

2009-Jan-13 16:00 UTC

[Rd] particulars of importing/loading libraries

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).

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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The contents of this email are for the named addressees ...{{dropped:19}}

Martin Morgan

2009-Jan-13 16:30 UTC

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[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"
>
>
> **********************************************************************
> Please consider the environment before printing this email or its
attachments.
> The contents of this email are for the named addressees ...{{dropped:19}}
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
-- 
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

Simon Urbanek

2009-Jan-14 01:50 UTC

head link

[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"
>
>
> **********************************************************************
> Please consider the environment before printing this email or its  
> attachments.
> The contents of this email are for the named addressees ...{{dropped: 
> 19}}
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>

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