R help - Oct 2008 - follow up on "[Rd] NAMESPACE & methods guidance, please" ( http://tolstoy.newcastle.edu.au/R/e4/devel/08/06/1901.html )

This is a follow-up on the discussion originally posted on the R-devel list (
http://tolstoy.newcastle.edu.au/R/e4/devel/08/06/1901.html ), as I have
encountered the exact same issue mentioned in Martin's email.   Here is a
simplified version of my problem:


##================================================================## I created a
package, say, "tmpA", with a NAMESPACE with Depend: and Imports:
org.Hs.eg.db and in a new session of R
> library(tmpA)
> foo
function ()
{

    require("org.Hs.eg.db")
    get("A GO TERM", org.Hs.egGO2ALLEGS)
}

> foo()
Error in as.environment(pos) : invalid object for 'as.environment' 
##================================================================

I fixed the problem by changing "get" explicitly to
"AnnotationDbi::get".  I'm just wondering what was the final
decision on the problem and if there are more elegant ways of handling this.

Thanks,

...Tao



_________________________________________________________________


50F681DAD532637!5295.entry?ocid=TXT_TAGLM_WL_domore_092008

Hi Tao -- 

Tao Shi <shitao at hotmail.com> writes:
> This is a follow-up on the discussion originally posted on the
> R-devel list (
> http://tolstoy.newcastle.edu.au/R/e4/devel/08/06/1901.html ), as I
> have encountered the exact same issue mentioned in Martin's email.
> Here is a simplified version of my problem:
>
>
> ##================================================================> ## I
created a package, say, "tmpA", with a NAMESPACE with Depend:
> and Imports: org.Hs.eg.db and in a new session of R
>
>> library(tmpA)
>> foo
>
> function ()
> {
>
>     require("org.Hs.eg.db")
>     get("A GO TERM", org.Hs.egGO2ALLEGS)
> }
>
>
>> foo()
>
> Error in as.environment(pos) : invalid object for 'as.environment' 
> ##================================================================>
>
> I fixed the problem by changing "get" explicitly to
> "AnnotationDbi::get".  I'm just wondering what was the final
> decision on the problem and if there are more elegant ways of
> handling this.
I think this is a matter of programming style.

Likely your package manipulates different annotation packages, so it
might make sense to Import: AnnotationDbi (or Depends:, but only if
the end user will need to directly use AnnotationDbi
functionality). In the NAMESPACE, you might then
importFrom(AnnotationDbi, get). All uses of 'get' inside your package
now see AnnotationDbi's 'get' methods.

Since you 'require' org.Hs.eg.db, it sounds like this is a package
that belongs in 'Suggests:' not 'Depends'.

Follow-ups might go to bioc-devel.

Martin


> Thanks,
>
> ...Tao
>
>
>
> _________________________________________________________________
>
>
> 50F681DAD532637!5295.entry?ocid=TXT_TAGLM_WL_domore_092008
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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