[BioC] missing content in limma documentation pdf

[Martin Morgan]

Martin Morgan wrote:
> Hi Torsten -- I believe that this is a shortcoming in Sweave as current
> in the R appropriate for Bioc 2.3 (unable to wrap commented lines, or
> lines without spaces) and so not readily 'fixed'. On the other hand,
> this is the reference manual and all detail can be found from within R,
> e.g.,
> 
>   ?duplicateCorrelation
> 
> The package maintainer might update the source code for the man pages,
> but this wouldn't have an effect on Bioc 2.3, which is not the current
> version.

Hmm, to follow through a bit on this, I wrongly blamed Sweave for
formatting, and underestimated the amount of work required to make pdf
versions of the manual 'pretty'. Sweave does not play a role in creating
the manual. Instead, the R tools for processing the vignette place the
usage section in a 'verbatim' tex environment (similarly for the
examples code, too, I think). Thus the 'fix' is for each package
maintainer to write 'man' pages that are consistent with reasonable
display of this formatting -- a fairly daunting task.

For the record, the way man pages are generated as pdf is

  R CMD Rd2dvi --pdf <pkg_name-or-Rd_file>

Martin
> 
> Martin
> 
> Torsten Waldminghaus wrote:
>> Dear all,
>>
>>  
>>
>> the limma documentation stored here:
>> http://www.bioconductor.org/packages/2.3/bioc/manuals/limma/man/limma.pd
>> f 
>>
>> has some lines being cut at the end of the page leading to loss of
>> sometimes important information (see for example p. 55 or 70). 
>>
>>  
>>
>>  
>>
>> Can somebody fix this or is there a full version somewhere?
>>
>>  
>>
>> Cheers,
>>
>> Torsten
>>
>>  
>>
>> Torsten Waldminghaus
>>
>> Department of Cell Biology
>>
>> Institute for Cancer Research
>>
>> Rikshospitalet-Radiumhospitalet-HF
>>
>> Ullernchaussen 70
>>
>> 0310 Oslo
>>
>> tel: 47-22935973
>>
>> fax: 47-22934580
>>
>> e-mail: Torsten.Waldminghaus at rr-research.no
>>
>> http://openwetware.org/wiki/User:Torsten_Waldminghaus
>>
>>  
>>
>>
>> 	[[alternative HTML version deleted]]
>>
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