From osklyar at maninvestments.com  Wed Jan 14 17:49:25 2009
From: osklyar at maninvestments.com (Sklyar, Oleg (London))
Date: Wed, 14 Jan 2009 16:49:25 -0000
Subject: [Rd] particulars of importing/loading libraries
In-Reply-To: <B4884C38-AB6A-40B3-A156-8698C28CD878@r-project.org>
References: <1A68FCB28DE72F4BA3B967E6506CCE43047DF583@mildnpexmb01.maninvestments.ad.man.com>
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	<1A68FCB28DE72F4BA3B967E6506CCE43047DF588@mildnpexmb01.maninvestments.ad.man.com>
	<17552B71-88D9-456D-84A4-EC9ACC6744A2@r-project.org>
	<1A68FCB28DE72F4BA3B967E6506CCE43047DF593@mildnpexmb01.maninvestments.ad.man.com>
	<B4884C38-AB6A-40B3-A156-8698C28CD878@r-project.org>
Message-ID: <1A68FCB28DE72F4BA3B967E6506CCE43047DF594@mildnpexmb01.maninvestments.ad.man.com>

Thank you Simon.

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 16:11
> To: Sklyar, Oleg (London)
> Cc: r-devel at r-project.org
> Subject: Re: [Rd] particulars of importing/loading libraries
> 
> 
> On Jan 14, 2009, at 10:52 , Sklyar, Oleg (London) wrote:
> 
> > Well, this is very reasonable and this is how it should be I would  
> > say. If it was consistent, there would be no problem as they would  
> > be easy to nail down. However, the problem is now that if I load  
> > pack3 only (which imports pack2 only) then as.POSIXct 
> exported from  
> > pack1 is NOT available for functions in pack3,
> 
> Because pack3 didn't request it.
> 
> 
> > but is available for calls from the global env (see example 
> below).  
> > It is obviously available for calls from functions in pack2 
> as there  
> > it is imported directly. Although, why also testPosix() of 
> pack2 is  
> > then available for calls from the global env as it was only loaded  
> > as import for pack3?
> >
> 
> Global environment is not encapsulated - you have access to anything  
> that has been attached - sort of implicitly importing anything that  
> has even been [exported and] attached (there is really no concept of  
> "importing" for the global environment, but the effect is 
> analogous).  
> This is a conceptual difference of the "interactive" use vs package  
> code. Unlike package code you don't know in advance what you will be  
> doing when you're working interactively, so I think it makes 
> sense to  
> assume that everything is implicitly imported.
> 
> Cheers,
> S
> 
> 
> > In my understanding if pack3 does not depend on pack1 directly,
> > functionality of pack1 should not be available anywhere apart from
> > functions called from pack2 as well as functions in pack2 should  
> > only be
> > available for calls by functions in pack3 but not in the 
> global env...
> > The semantics seems to be broken here, is it not?
> >
> >> library(pack3)
> > Loading required package: pack2
> > Loading required package: pack1
> >> testPosix() ## from pack2
> > [1] "2009-01-13 15:29:50 UTC"
> > [1] "POSIXt"  "POSIXct"
> > [1] "2009-01-13 15:29:50 UTC"
> >> testPosix2()
> > Error in as.POSIXct.default(testPosixVal) :
> >  do not know how to convert 'testPosixVal' to class "POSIXlt"
> >> as.POSIXct(pack1::testPosixVal)
> > [1] "2009-01-13 15:29:50 UTC"
> >
> >
> >
> > 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 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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[Rd] particulars of importing/loading libraries
Sklyar, Oleg (London