From ripley at stats.ox.ac.uk  Mon Jan 31 20:48:33 2011
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Mon, 31 Jan 2011 19:48:33 +0000 (GMT)
Subject: [Rd] Warning: you may need to use R-patched with recent R distros
Message-ID: <alpine.LFD.2.02.1101311928400.30471@gannet.stats.ox.ac.uk>

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



[Rd] Warning: you may need to use R-patched with recent R distros
Prof Brian Ripley