[R] R debugging options
Prof Brian Ripley
ripley at stats.ox.ac.uk
Sat Apr 22 10:07:33 CEST 2006
On Sat, 22 Apr 2006, Prof Brian Ripley wrote:
> On Fri, 21 Apr 2006, John Fox wrote:
>
>> Dear Spencer,
>>
>> I wasn't aware of getFunctions(), though I've now taken a look at it. It's
>> pretty similar to listFunctions() (from my email to the list), except that
>> getFunctions() uses exists() rather than is.function() to test whether an
>> object is a function. There must be a reason for this, but I can't think
>> what it is, since in both cases the vector of object names shouldn't include
>> nonexistent objects.
>
> John,
>
> Your code uses eval(parse()) to find the object, and that is somewhat
> clumsy. A more usual way would be
>
> function(x) is.function(get(x, envir=envir))
>
> and exists() can shortcircuit that by asking for a particular 'mode'.
> There's a prototypical version in utils::ls.str of using exists(), and
> a simpler yet more powerful version than either of yours would be
>
> listFunctions <- function(all.names=FALSE, envir=.GlobalEnv){
> # all.names=TRUE: include names beginning with "."
> # envir: environment to search
> envir <- as.environment(envir)
> z <- ls(envir=envir, all.names=all.names)
> z[sapply(z, function(x) exists(x, mode="function",
> envir=envir, inherits=FALSE))]
> }
Aargh, sapply does not simplify if the result is of length 0. Use
unlist(lapply()) instead (which is incidentally slightly more efficient).
> Note that inherits=FALSE is needed, for although the named object exists,
> exists() has been told to search for a function of that name and might
> find one elsewhere. (ls.str appears to have that wrong.)
>
> Now for some pickiness: what is a 'function'? This lists "$" as a
> function, which it is, but it is not a closure. Although
> exists(mode="closure") would appear to be documented to differentiate, it
> does not and so one needed function(x) typeof(get(x, ...)) == "closure".
>
> Brian
>
>>
>> Regards,
>> John
>>
>> --------------------------------
>> John Fox
>> Department of Sociology
>> McMaster University
>> Hamilton, Ontario
>> Canada L8S 4M4
>> 905-525-9140x23604
>> http://socserv.mcmaster.ca/jfox
>> --------------------------------
>>
>>> -----Original Message-----
>>> From: Spencer Graves [mailto:spencer.graves at pdf.com]
>>> Sent: Friday, April 21, 2006 11:21 AM
>>> To: John Fox
>>> Cc: 'Larry Howe'; r-help at stat.math.ethz.ch; Philippe Grosjean
>>> Subject: Re: [R] R debugging options
>>>
>>> Regarding a function that lists functions, have you
>>> considered "getFunctions" in library(svIDE)? You need to
>>> provide the argument, as
>>> in "getFunctions(1)"; "getFunctions()" returns an error message.
>>>
>>> Beyond this, the "objects" function in S-Plus (at
>>> least version 6.2) has a "classes" argument, which the R
>>> 2.2.1 implementation does not have. It doesn't look like it
>>> would be too difficult to add such an argument to "objects"
>>> in R, but I have not been in a position to volunteer to do
>>> it, and without that, I didn't feel it was appropriate for me
>>> to suggest it.
>>>
>>> hope this helps,
>>> spencer graves
>>>
>>> John Fox wrote:
>>>
>>>> Dear Larry,
>>>>
>>>> I'm not aware of an existing function that lists functions,
>>> but here's
>>>> a simple solution:
>>>>
>>>> listFunctions <- function(all.names=FALSE, envir=.GlobalEnv){
>>>> # all.names=TRUE: include names beginning with "."
>>>> # envir: environment to search
>>>> Objects <- objects(envir, all.names=all.names)
>>>> if (length(Objects) == 0) Objects
>>>> else names(which(sapply(Objects,
>>>> function(object) is.function(eval(parse(text=object),
>>>> envir=envir)))))
>>>> }
>>>>
>>>> Getting mtrace() to use the function names returned by
>>> listFunctions()
>>>> is a bit tricky, because of the way mtrace() evaluates its
>>> arguments.
>>>> You could do something like the following:
>>>>
>>>> for(f in listFunctions()) mtrace(char.fname=f)
>>>>
>>>> Perhaps someone else knows of an existing or better solution.
>>>>
>>>> I hope this helps,
>>>> John
>>>>
>>>> --------------------------------
>>>> John Fox
>>>> Department of Sociology
>>>> McMaster University
>>>> Hamilton, Ontario
>>>> Canada L8S 4M4
>>>> 905-525-9140x23604
>>>> http://socserv.mcmaster.ca/jfox
>>>> --------------------------------
>>>>
>>>>
>>>>> -----Original Message-----
>>>>> From: r-help-bounces at stat.math.ethz.ch
>>>>> [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Larry Howe
>>>>> Sent: Tuesday, April 18, 2006 12:46 PM
>>>>> To: r-help at stat.math.ethz.ch
>>>>> Subject: Re: [R] R debugging options
>>>>>
>>>>> On Monday April 17 2006 21:08, Francisco J. Zagmutt wrote:
>>>>>
>>>>>> RSiteSearch("debug") or RSiteSearch("debugging") will give
>>>>>
>>>>> you a lot
>>>>>
>>>>>> or relevant information. I personally use library(debug)
>>>>>
>>>>> extensivelly
>>>>>
>>>>>> and it should do all the taks you asked about. There is a
>>>>>
>>>>> nice article
>>>>>
>>>>>> describing the debug lilbrary in the 2003/3 issue of R News
>>>>>> http://cran.r-project.org/doc/Rnews/Rnews_2003-3.pdf
>>>>>>
>>>>>> Cheers
>>>>>>
>>>>>> Francisco
>>>>>
>>>>> Wow! That is a great package. I think it does all I need.
>>>>>
>>>>> Is there a way to turn on debugging for all loaded functions?
>>>>> My source file contains many functions and I would prefer
>>> not to have
>>>>> to mtrace() each one.
>>>>> Something like
>>>>>
>>>>>
>>>>>> mtrace(how_do_I_get_a_list_of_all_loaded_functions)
>>>>>
>>>>> ?
>>>>>
>>>>> Larry
>>>>>
>>>>> ______________________________________________
>>>>> R-help at stat.math.ethz.ch mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>> PLEASE do read the posting guide!
>>>>> http://www.R-project.org/posting-guide.html
>>>>
>>>>
>>>> ______________________________________________
>>>> R-help at stat.math.ethz.ch mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>> PLEASE do read the posting guide!
>>> http://www.R-project.org/posting-guide.html
>>
>> ______________________________________________
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>>
>
>
--
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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