From jon.clayden at gmail.com  Thu Mar 15 22:24:17 2012
From: jon.clayden at gmail.com (Jon Clayden)
Date: Thu, 15 Mar 2012 21:24:17 +0000
Subject: [Rd] Dealing with printf() &c. in third-party library code
In-Reply-To: <4F61786B.6030200@fhcrc.org>
References: <CAM9CR=2iwS1E3TFnh5y-SRCh5p3KEtSD1ChO7bVpXgMsRV_PrQ@mail.gmail.com>
	<4F61786B.6030200@fhcrc.org>
Message-ID: <CAM9CR=2493iX8V4-5WXSC4461WoSVkWY_USs+J=RAYTCS-gY0w@mail.gmail.com>

Martin,

Thanks for your reply. I wonder if you'd be willing to post your
"my_fprintf" function, since I'm struggling to get around needing to
use the "stdout" and "stderr" symbols completely. This function has
the right effect...

void rniftyreg_fprintf (FILE *stream, const char *format, ...)
{
   va_list args;
   va_start(args, format);

   if (stream == stdout)
       Rvprintf(format, args);
   else if (stream == stderr)
       REvprintf(format, args);
   else
       vfprintf(stream, format, args);

   va_end(args);
}

... but the R CMD check info message still arises because stdout and
stderr still appear. I'm struggling to see how to get around this
without doing something really ugly, like casting integers to FILE*
pointers.

All the best,
Jon


On 15 March 2012 05:04, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> On 03/14/2012 05:15 AM, Jon Clayden wrote:
>>
>> Dear all,
>>
>> I recognise the reason for strongly discouraging use of printf() and
>> similar C functions in R packages, but I wonder what people do in
>> practice about third-party code which may be littered with such calls.
>> I maintain a package (RNiftyReg) which provides an R interface to a
>> third-party library which contains hundreds of calls to printf(...),
>> fprintf(stderr,...) and similar. It seems to me that there are several
>> possible approaches, but all have their issues:
>>
>> 1. Replace all such calls with equivalent Rprintf() calls, using
>> compiler preprocessing directives to ensure the library does not
>> become incompatible with other code. For example,
>>
>> #ifdef RNIFTYREG
>> Rprintf(...);
>> #else
>> printf(...);
>> #endif
>>
>> This will be very time-consuming if there are lots of calls, and also
>> makes the code very untidy and much harder to update when a new
>> version of the upstream library is released.
>>
>> 2. Remove all such calls from the code altogether, or comment them
>> out. The problem here is that doing this safely is hard, because the
>> call could be part of an "if" statement or similar. For example,
>>
>> if (test)
>> ?printf("Something");
>> do_something_important;
>>
>> If the middle line here is removed, then the last line becomes
>> (erroneously) conditioned on the test. Plus, once again, you are
>> introducing a lot of small changes to the library itself.
>>
>> 3. Redefine printf to use Rprintf, viz.
>>
>> #ifdef RNIFTYREG
>> #include<R.h>
>> #define printf Rprintf
>> #endif
>>
>> This will compile as long as the R function is a drop-in replacement
>> for the original function, which I believe is true for Rprintf (vs.
>> printf), but isn't true for Calloc (vs. calloc), for example. And I'm
>> not sure whether this approach can be used to deal with cases of the
>> form fprintf(stderr,...), where stderr would need to be redefined.
>> This approach requires only modest changes to the library itself, but
>> may be fragile to future changes in R.
>>
>> Are there any other (better?) alternatives? Any thoughts or advice
>> would be appreciated.
>
>
> In Makevars, I add -Dfprintf=my_fprintf to the pre-processor flags and then
> implement my_fprintf in a separate source file. This means that the source
> code of the 3rd party library is not touched, and there is some scope for
> re-mapping or otherwise intercepting function arguments. For abort and
> error, I throw an error that encourages the user to save and quit
> immediately, though this is far from ideal. I too would be interested in
> better practices for dealing with this, short of whole-sale modification of
> the third-party library.
>
> Martin
>
>>
>> All the best,
>> Jon
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793



[Rd] Dealing with printf() &c. in third-party library code
Jon Clayden