R devel - Sep 2002 - setGeneric(); R CMD check

1. Is it always the case that when defining generic functions in
   a package, the package needs to be installed as a binary package
   to avoid having the generic functions in the .GlobalEnv?

2. Defining a generic function in a "non-binary" package triggers 
   a check warning

     $ R CMD check ...
     ...
     * checking for code/documentation mismatches ... WARNING
     Objects with usage in documentation object 'dbApply' but missing
from code:
     [1] "dbApply"

   It seems that the generic function dbApply lives in the .GlobalEnv when
   the package is attached (w. library), but not in the package's
environment.
   I presume that's why check triggers the warning.

   Is this the case?

*If* this is the case (i.e., packages with setGeneric()s need to be installed
as binaries), perhaps it should be documented somewhere.

... or am I missing something very basic?
> version
         _                           
platform i686-pc-linux-gnu           
arch     i686                        
os       linux-gnu                   
system   i686, linux-gnu             
status   Under development (unstable)
major    1                           
minor    6.0                         
year     2002                        
month    09                          
day      09                          
language R

-- 
David A. James
Statistics Research, Room 2C-253            Phone:  (908) 582-3082       
Bell Labs, Lucent Technologies              Fax:    (908) 582-3340
Murray Hill, NJ 09794-0636
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David James wrote:
> 
> 1. Is it always the case that when defining generic functions in
>    a package, the package needs to be installed as a binary package
>    to avoid having the generic functions in the .GlobalEnv?
By "binary", meaning "INSTALL --save" or equivalent?

Yes, and the symptom you mentioned is rather mild, compared to what will
often happen!  Any of the computations that default to assigning
metadata to the global environment will cause problems (setMethod,
setClass, ...) in a default installation, unless all such computations
are wrapped in a function call that can be re-directed from the
.First.lib function to the correct environment.

It's not likely to be worth the effort.

For the present version of R, the simplest approach is probably for the
programmer to arrange for an installation with a saved image, either
through the option to INSTALL or by putting a file "install.R" (an
empty
file will do) in the top source directory of the package.

For the next version, we should try to make the process more automatic,
although the only way that would always work seems to be by making
--save the default to INSTALL.
> 
> 2. Defining a generic function in a "non-binary" package triggers
>    a check warning
> 
...................

As mentioned, the "CMD check"  problem may be the least of it!

The following snippet will _apparently_ install with or without --save:

### Dummy Package
require("methods")

foo <- function(x)x

setGeneric("foo")

setMethod("foo", "character", function(x)
paste("++", x))
###

But in the default install, it fails (annoyingly) when the library is
attached, because the assignment of foo is not in the search list, so
setGeneric doesn't find any definition of "foo".


R> library(DummyPackage)
Loading required package: methods 
Error in setGeneric("foo") : Must supply a function skeleton,
explicitly
or via an existing function


It's possible to work around most of the specific problems, but my
feeling is that the natural semantics for the programmer is that  the
same source code should work basically the same way, whether being
sourced into the global environment for initial testing or being
installed as a package.
> *If* this is the case (i.e., packages with setGeneric()s need to be
installed
> as binaries), perhaps it should be documented somewhere.
> 
Yes.  I'll add it to the online help for INSTALL (& the extensions
document?).

John
> --
> David A. James
> Statistics Research, Room 2C-253            Phone:  (908) 582-3082
> Bell Labs, Lucent Technologies              Fax:    (908) 582-3340
> Murray Hill, NJ 09794-0636
>
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> r-devel mailing list -- Read
http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
> Send "info", "help", or "[un]subscribe"
> (in the "body", not the subject !)  To:
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>
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-- 
John M. Chambers                  jmc@bell-labs.com
Bell Labs, Lucent Technologies    office: (908)582-2681
700 Mountain Avenue, Room 2C-282  fax:    (908)582-3340
Murray Hill, NJ  07974            web: http://www.cs.bell-labs.com/~jmc
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