[Rd] Recent TeX changes and R/package manuals

[Prof Brian Ripley]

As some of you will be aware, TeXLive 2009 was released last month 
having blocked updates on earlier versions since May.  This has lead 
to a flood of updates of LaTeX packages, as a result of which the 
PDF manuals of R 2.10.0 and earlier will no longer build, for two 
separate reasons.

For MiKTeX users: at least version 2.8 (the current one) has the same 
updates (a week or so later) and has the same issues.

After some workarounds, 2.10.1 RC and R-devel do build their manuals 
for me on TL2009 on Linux, MacTeX 2009 (a TL2009 derivative) on Mac OS 
X and current MiKTeX 2.8 on Windows.

As far as I can tell, the following CRAN package manuals have been 
affected:

   distrMod, RCurl, RGtk2, SparseM, VIM, bit, ggplot2, operators,
   relations, spam, tensorA

(and only distrMod fatally).

Given the current pace of change (ca 100 updates/week on 'only' 2000 
TL packages), more things may pop out of the woodwork.


For the curious and cognescenti:

(i) hyperref is having problems with markup in \section titles, which 
'methods' and 'distrMod' had.  I've added a warning to the R-exts 
manual.


(ii) there have been intermittent problems with (LaTeX) special 
characters in indices.  But (hyperref 6.79d)

   Full support of makeindex’s encap feature (e.g.
   \index{alpha|textbf}). \hyperpage and the formatting command are
   cascaded via \hyperindexformat. Internally \index{alpha|textbf} is
   transferred to \index{alpha|hyperindexformat{\textbf}}.
   \hyperindexformat calls the formatting command in its first argument
   with the page range as argument that is put into \hyperpage. The
   formatting command may call \hyperpage itself, it will be disabled
   automatically to prevent nested \hyperpage commands.

has broken '|' as an index item ('||' was already broken) so I added 
some special-casing (this does look like a bug in hyperref).  Also 
some uses of '%' (ggplot2, operators, relations).


(iii) some LaTeX style files are no longer in TL2009. e.g. 
floatflt.sty (used by packages EffectiveDose, gWidgets, gWidgetsWWW, 
monoProc, pmg).

-- 
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