On Mon, Dec 14, 2009 at 09:24:12AM +0100, Kurt Hornik wrote:
> >>>>> Peter Dalgaard writes:
[...]
> > 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...
>
> Well, I am sure I had good reasons when I wrote the code many years ago,
> but of course I no longer recall what they were.
>
> Did you try the effect of removing the length(formals(f)) test?
I understand this as the question, what is the influence of the following patch
(indented by two spaces).
diff --minimal -U 3 -r R-devel_2009-12-13/src/library/tools/R/QC.R
R-devel_length_formals/src/library/tools/R/QC.R
--- R-devel_2009-12-13/src/library/tools/R/QC.R 2009-10-27
02:59:10.000000000 +0100
+++ R-devel_length_formals/src/library/tools/R/QC.R 2009-12-14
18:45:55.000000000 +0100
@@ -398,7 +398,7 @@
functions_in_code <-
Filter(function(f) {
f <- get(f, envir = code_env)
- is.function(f) && (length(formals(f)) > 0L)
+ is.function(f)
},
objects_in_code)
## Sourcing all R code files in the package is a problem for base,
Since i do not know this part of R code, i simply applied the patch to the
current R-devel and run "make" and "make check" (both OK) and compared
the output of
R CMD check XML_2.6-0.tar.gz
R CMD check randomForest_4.5-33.tar.gz
R CMD check tree_1.0-27.tar.gz
R CMD check survival_2.35-7.tar.gz
with R being both original R-devel and the modified one. The results were
identical
in all four cases (empty diff) on two Linux machines (CentOS and openSUSE).
On the other hand, for the package
http://www.cs.cas.cz/~savicky/R-devel/something_0.0.0.tar.gz
which demonstrates the problem, the modified R detected the code/doc mismatch.
The diff of the two outputs of R CMD check was
[savi...@uivtx test]$ diff original modified
35c35,42
< * checking for code/documentation mismatches ... OK
---
> * checking for code/documentation mismatches ... WARNING
> Codoc mismatches from documentation object 'testCore':
> testCoreNA
> Code: function()
> Docs: function(verbose = 0)
> Argument names in docs not in code:
> verbose
>
39a47,50
> WARNING: There was 1 warning, see
> /home/savicky/tmp/test/something.Rcheck/00check.log
> for details
>
Petr Savicky.
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