Re: [Rd] R CMD check may not detect a code/documentation mismatch

From: Peter Dalgaard <p.dalgaard_at_biostat.ku.dk>
Date: Sun, 13 Dec 2009 13:59:55 +0100

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...

-- 
    O__  ---- Peter Dalgaard             ุster Farimagsgade 5, Entr.B
   c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
  (*) \(*) -- University of Copenhagen   Denmark      Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard_at_biostat.ku.dk)              FAX: (+45) 35327907

______________________________________________
R-devel_at_r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Received on Sun 13 Dec 2009 - 13:02:59 GMT

This archive was generated by hypermail 2.2.0 : Mon 14 Dec 2009 - 09:21:08 GMT