R devel - Dec 2009 - R CMD check may not detect a code/documentation mismatch

For the package at
  http://www.cs.cas.cz/~savicky/R-devel/something_0.0.0.tar.gz
which is a minor part of some other package only to demonstrate the
problem, i get (under R version 2.11.0 Under development 2009-12-12 r50714
and also under R-2.9.2, openSUSE 11.1 (x86_64) and CentOS release 5.2)

  R CMD check something_0.0.0.tar.gz

  ...
  * checking Rd files ... OK
  * checking Rd metadata ... OK
  * checking Rd cross-references ... OK
  * checking for missing documentation entries ... OK
  * checking for code/documentation mismatches ... OK
  * checking Rd \usage sections ... OK
  * checking examples ... NONE
  * checking PDF version of manual ... OK

although the package code contains

  testCoreNA <- function()

and the documentation contains

  \usage{
  testCoreClass(verbose=0)
  testCoreAttrEval(verbose=0)
  testCoreReg(verbose=0)
  testCoreNA(verbose=0)
  }

There is a mismatch between code and documentation of testCoreNA(). Is the 
problem caused by having four entries in \usage{} section?

Petr Savicky.

Petr Savicky wrote:
> For the package at
>   http://www.cs.cas.cz/~savicky/R-devel/something_0.0.0.tar.gz
> which is a minor part of some other package only to demonstrate the
> problem, i get (under R version 2.11.0 Under development 2009-12-12 r50714
> and also under R-2.9.2, openSUSE 11.1 (x86_64) and CentOS release 5.2)
> 
>   R CMD check something_0.0.0.tar.gz
> 
>   ...
>   * checking Rd files ... OK
>   * checking Rd metadata ... OK
>   * checking Rd cross-references ... OK
>   * checking for missing documentation entries ... OK
>   * checking for code/documentation mismatches ... OK
>   * checking Rd \usage sections ... OK
>   * checking examples ... NONE
>   * checking PDF version of manual ... OK
> 
> although the package code contains
> 
>   testCoreNA <- function()
> 
> and the documentation contains
> 
>   \usage{
>   testCoreClass(verbose=0)
>   testCoreAttrEval(verbose=0)
>   testCoreReg(verbose=0)
>   testCoreNA(verbose=0)
>   }
> 
> There is a mismatch between code and documentation of testCoreNA(). Is the 
> problem caused by having four entries in \usage{} section?
Hmm, looks more like a thinko in this code inside codoc():

     functions_in_code <- Filter(function(f) {
         f <- get(f, envir = code_env)
         is.function(f) && (length(formals(f)) > 0L)
     }, objects_in_code)

which, further down the line, causes functions with no formal arguments 
to be skipped when compared to the usage section.

Browse[2]>
debug: ind <- (!functions %in% functions_to_be_ignored & functions %in%
     functions_in_code)
Browse[2]> functions
[1] "testCoreClass"    "testCoreAttrEval"
"testCoreReg"
"testCoreNA"
Browse[2]>
debug: bad_functions <- mapply(functions[ind], exprs[ind], FUN = 
function(x,
     y) check_codoc(x, as.pairlist(as.alist.call(y[-1L]))), SIMPLIFY = 
FALSE)
Browse[2]> ind
[1]  TRUE  TRUE  TRUE FALSE

I.e. testCoreNA is never tested by check_codoc. There may of course be a 
rationale for this, but it escapes me...


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