Re: [Rd] R CMD check may not detect a code/documentation mismatch
[orig. correspondence below]
Brian and Kurt have been sinking their teeth further into this. It
turned out that there was a gotcha with the .Primitive functions like
`:`, `.C`, etc., for which formals() always returns NULL. However,
replacement with a check for typeof(f) == "closure" made things work,
and revealed a handful of undetected issues in CRAN packages.
So this has now been committed to r-devel. Thanks for chasing this up.
-pd
Petr Savicky wrote:
> 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
> 02:59:10.0 +0100
> +++ R-devel_length_formals/src/library/tools/R/QC.R 2009-12-14
> 18:45:55.0 +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.
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907
__
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Re: [Rd] R CMD check may not detect a code/documentation mismatch
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
02:59:10.0 +0100
+++ R-devel_length_formals/src/library/tools/R/QC.R 2009-12-14
18:45:55.0 +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.
__
R-devel@r-project.org mailing list
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Re: [Rd] R CMD check may not detect a code/documentation mismatch
Kurt Hornik wrote:
>> Peter Dalgaard writes:
>
>> 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...
>
> 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?
Not yet. Priorities
-p
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907
__
R-devel@r-project.org mailing list
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Re: [Rd] R CMD check may not detect a code/documentation mismatch
> Peter Dalgaard writes:
> 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...
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?
-k
> --
> O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
>c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
> (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
> ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD check may not detect a code/documentation mismatch
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 Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] 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.
__
R-devel@r-project.org mailing list
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