Re: [Rd] R-devel on FreeBSD: new C99 functions don't build

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Fri, 18 May 2012 15:15:48 +0100

On 15/05/2012 20:45, Rainer Hurling wrote:
> On 15.05.2012 20:49 (UTC+1), Murray Stokely wrote:
>> On Tue, May 15, 2012 at 10:05 AM, Rainer Hurling<rhurlin_at_gwdg.de> wrote:
>>> About April 25th, there had been some changes within R-devel's
>>> src/nmath/pnbeta.c (and probably some other relevant places) and now
>>> building R-devel on FreeBSD 10.0-CURRENT (amd64) with gcc-4.6.4 and
>>> math/R-devel (selfmade forked port from math/R) fails like this:
>>
>>> It seems, that at least one new C99 function (log1pl) is introduced in
>>> R-devel, see
>>>
>>> src/nmath/pnbeta.c:l95
>>> return (double) (log_p ? log1pl(-ans) : (1 - ans));
>>
>> AFAIK, Bruce Evans is not happy with the numerical accuracy of other
>> open-source implementations of log1pl and so has blocked their
>> inclusion in FreeBSD pending work on a better implementation.
>>
>> Can you put a conditional FreeBSD check here and use log1p instead of
>> log1pl instead as a workaround?
>>
>> I can admire the insistence on correctness from the FreeBSD libm
>> maintainers for their technical purity, but it can be a bit of a pain
>> for things like this.
>>
>> - Murray
>
> I read about this discussion and in principle I concur with your
> opinion. As a scientist I tend to expect greatest possible correctness
> from a statistical routine, especially when it uses long double format.
>
> As a quick and dirty workaround I applied the following patch:
>
>
> --- src/nmath/pnbeta.c.orig 2012-04-25 17:55:14.000000000 +0200
> +++ src/nmath/pnbeta.c 2012-05-15 20:58:26.000000000 +0200
> @@ -92,7 +92,11 @@
> else {
> if(ans > 1 - 1e-10) ML_ERROR(ME_PRECISION, "pnbeta");
> if (ans > 1.0) ans = 1.0; /* Precaution */
> +#if !defined(__FreeBSD__)
> return (double) (log_p ? log1pl(-ans) : (1 - ans));
> +#else
> + return (double) (log_p ? log1p(-ans) : (1 - ans));
> +#endif /* FreeBSD */
> }
> }
>
>
> It builds and installs fine now and I hope there are no side effects ...

Note though that R has *required* C99 compliance for quite a while, and that is not now even the current C standard. Using an OS that fails to comply to a 12-year-old standard is your own choice ... and you get the choice of using an equally old version of R.

I've added log1pl to the depressing list of FreeBSD workarounds: untested as I currently don't have access to a FreeBSD setup.

However, I think this has to come to an end: if a project such as Mingw-w64 can make the effort to supply a great deal of the C99 functions missing from their OS then we must expect FreeBSD to do likewise.

> Thank you for the quick answer and your advice,
> Rainer

-- 
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

______________________________________________
R-devel_at_r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Received on Fri 18 May 2012 - 14:18:36 GMT

This quarter's messages: by month, or sorted: [ by date ] [ by thread ] [ by subject ] [ by author ]

All messages

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Tue 22 May 2012 - 10:21:40 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-devel. Please read the posting guide before posting to the list.

list of date sections of archive