[Rd] Warning: you may need to use R-patched with recent R distros
Prof Brian Ripley
ripley at stats.ox.ac.uk
Mon Jan 31 21:18:01 CET 2011
On Mon, 31 Jan 2011, Ken.Williams at thomsonreuters.com wrote:
> For the complex-numbers bug, do you know a reliable way (besides looking
> at version numbers) to determine whether the bug is present or absent in a
> given build?
I know a way: See tests/complex.R in R-devel.
z <- 0.2853725+0.3927816i
z2 <- z^(1:20)
z3 <- z^-(1:20)
z0 <- cumprod(rep(z, 20))
stopifnot(all.equal(z2, z0), all.equal(z3, 1/z0))
## z^3 had value z^2 ....
> I don't know what version of gcc was used in my build nor the optimization
> flags, so I did a few test exponentiations z^n and the results look okay,
> but maybe I'm not tickling the right bits.
> Ken Williams
> Senior Research Scientist
> Thomson Reuters
> Phone: 651-848-7712
> ken.williams at thomsonreuters.com
> On 1/31/11 1:48 PM, "Prof Brian Ripley" <ripley at stats.ox.ac.uk> wrote:
>> Two things have emerged in testing on x86_64 Fedora 14 which mean that
>> a recent R-patched is probably needed.
>> 1) That OS uses zlib 1.2.5: that claims to be binary-compatible with
>> zlib 1.2.3 but is not, as we found (painfully) on Windows. The remedy
>> was to remap _all_ the symbols in R's own copy of zlib (not just those
>> zlib arranged to remap).
>> The symptoms were crashes using packages XML and rgoobi (both of which
>> link to zlib) and incorrect results in RJaCGH (which contains a copy
>> of zlib). There may well be other problems ....
>> 2) Fedora 14 uses gcc 4.5.1. With CFLAGS containing the default -O2
>> or higher, HAVE_C99_COMPLEX was detected as false because there is a
>> (genuine) incompatibility between types Rcomplex and C99's double
>> complex. This means that R's fallback code is used, and regretably
>> that contains a serious bug in an 'optimization' by a colleague, so
>> z^n is incorrect for most complex z and integer n (and has been since
>> 2.10.0). The remedy is to use R-patched or R-devel, or only optimize
>> to -O.
>> We've also seen incorrect results from package mvtnorm when C
>> optimization was -O3.
>> The upshot is that there is likely to be a 2.12.2 to fix these issues.
>> 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
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
More information about the R-devel