From ripley at stats.ox.ac.uk  Sun Oct 11 14:45:05 2009
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Sun, 11 Oct 2009 13:45:05 +0100 (BST)
Subject: [Rd] Possible bug in the Rd parser?
In-Reply-To: <1255258638.4257.10.camel@ubuntu>
References: <1255176462.9627.43.camel@ubuntu> <4AD0D19D.8020607@stats.uwo.ca>
	<4AD0D539.3000506@stats.uwo.ca> <1255258638.4257.10.camel@ubuntu>
Message-ID: <alpine.LFD.2.00.0910111334170.21398@gannet.stats.ox.ac.uk>

On Sun, 11 Oct 2009, Mathieu Ribatet wrote:

> Thanks Duncan for all these answers. Indeed I should have checked that
> the "cases" environment was provided by Rd.sty. Mea culpa.
>
> The good point is that before 2.10.0 alpha "R CMD check" finished
> without any error but the output was wrong - because of the cases
> environment as you said. Now it fails and this is a good point as I,
> maybe others??, usually don't have a look at "mypkg-manual.pdf" but only
> at the html version of it.

Well, the recommended procedure has long been to look at the package 
PDF manual (which R CMD check leaves around for that purpose), and 
indeed this was (and still is) in the checklist in section 1.5 for 
'Writing R Extensions'.

However, please do look at *all* of text, HTML and PDF versions of the 
help, as this will help us to refine the rendering.   For example, one 
thing we have found recently is that tabs in the .Rd files are not 
being expanded as before and so alignment (especially in \usage and 
\examples sections) was off.  (We may be able to change that one 
before release, but it is an example of something that was in none of 
the main R help files and so took several weeks to spot.)

>
> Cheers,
> Mathieu
>
> Le samedi 10 octobre 2009 ? 20:40 +0200, Duncan Murdoch a ?crit :
>> On 10/10/2009 2:25 PM, Duncan Murdoch wrote:
>>> On 10/10/2009 8:07 AM, Mathieu Ribatet wrote:
>>>> Dear list,
>>>>
>>>> I got an automatic email complaining than some of my packages didn't
>>>> pass 'R CMD check' for R-2.10.0 alpha anymore. Both of them make use of
>>>> the "cases" LaTeX environment.
>>>>
>>>> Inspecting the log outputs I got:
>>>>
>>>>         LaTeX errors when creating PDF version.
>>>>         This typically indicates Rd problems.
>>>>         LaTeX errors found:
>>>>         ! Misplaced alignment tab character &.
>>>>
>>>> I noticed that the Rd parser changed quite recently and that '#', '_'
>>>> and '&' must not be escaped according to "Writing R extensions".
>>>> However, the problematic .Rd portion seems (to me) OK
>>>>
>>>>         \deqn{\theta(h) =
>>>>             \begin{cases}
>>>>             u_\beta \left(\mu +  \frac{\nu(h)}{\Gamma(1 - \xi)}
>>>>         \right),&\xi \neq 0\\
>>>>             \exp\left(\frac{\nu(h)}{\sigma}\right),&\xi = 0
>>>>             \end{cases}
>>>>           }{u_beta (mu + nu(h) / Gamma(1 - \xi)), if \xi < 1,
>>>>             exp(nu(h)/sigma), otherwise}
>>>>
>>>
>>> One more followup:  the problem appears to be in the "cases"
>>> environment.  If I rewrite that block using "array" instead, things are
>>> fine:
>>>
>>>          \deqn{\theta(h) =
>>>              \left\{\begin{array}{ll}
>>>              u_\beta \left(\mu +  \frac{\nu(h)}{\Gamma(1 - \xi)}
>>>          \right),&\xi \neq 0\\
>>>              \exp\left(\frac{\nu(h)}{\sigma}\right),&\xi = 0
>>>              \end{array}\right.
>>>            }{u_beta (mu + nu(h) / Gamma(1 - \xi)), if \xi < 1,
>>>              exp(nu(h)/sigma), otherwise}
>>>
>>> This makes me think it's a bug in the LaTeX package that provides
>>> "cases", or a conflict with our Rd.sty file, but I don't know which.
>>
>> And the final answer:  the "cases" environment is in the amsmath
>> package, which is not used by R.  You need to use regular LaTeX, not
>> fancy stuff like that.  (There's a \cases macro in LaTex, which doesn't
>> know what to do with alignment tabs:  that's why you got the error you did.)
>>
>> Duncan Murdoch
> -- 
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-- 
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)
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[Rd] Possible bug in the Rd parser?
Prof Brian Ripley