On Wed, 17-08-2016, at 15:08, Sean Davis <seand...@gmail.com> wrote:
>> On Aug 17, 2016, at 8:55 AM, Martin Morgan <martin.mor...@roswellpark.org>
>> wrote:
>>
>> On 08/17/2016 07:02 AM, Henrik Bengtsson wrote:
>>> R CMD build, which is what triggers vignette building, only supports one
>>> output file (HTML or PDF) per vignette. It will basically ignore duplicate
>>> output formats. This is by design / legacy reasons. Technically it wouldn't
>>> be hard to add support for multiple output formats, but that would require
>>> changes to R itself - I think it could be a useful feature.
>>>
>>> A related question is where some prefer to have access to also the
>>> intermediate plain Markdown / TeX rather than the final HTML / PDF product,
>>> e.g. because they work better with screen readers.
>>>
>>> The only way I see you can have a PDF and a HTML version at the same time
>>> is to create to identical vignettes each outputting a specific format.
>>
>> A consideration from the build machine perspective is the cost to process
>> the vignettes, in particular the code chunks. These would be done across
>> platforms and vignettes, because the build system wouldn't know about the
>> trickery you're engaged in.
>>
>> Also from the end user perspective I don't think having two vignettes with
>> identical content is particularly helpful; as a user I wouldn't be confident
>> that they were equally current (however adeptly the duplication of content
>> were implemented).
>>
>> Personally, I think the HTML presentation is much more conducive to the way
>> vignettes are used.
>
> And with some CSS trickery (may not even be needed if basing things on an
> established CSS framework), an HTML vignette can be rendered in a very nice
> printable form if folks want to print it.
>
> http://stackoverflow.com/a/12303057/459633
>
Thanks Sean, didn't know about that.
But then, doesn't this somehow defeats part of the purpose (or the spirit)
of R markdown: a single file, with low barrier of entry, that allows you to
produce HTML, PDF (and epub) just by calling one or another function in the
call to render? (Context: after having used LaTeX for maaaany years, I am
finding the markdown experience painful and disconcerting; the idea of
handling CSS trickery looks like additional pain and suprises :-).
As the one producing the vignette, what do I gain from inserting a link in
the HTML vignette that points to a place where I've left the PDF (produced
using pdf_document or similar)? (Aside from not inserting the link and not
having to produce the PDF, which can be automated via hooks or similar).
Best,
R.
> Sean
>
>
>>
>> Martin
>>
>>
>>>
>>> Henrik
>>>
>>> On Aug 17, 2016 12:17, "Ramon Diaz-Uriarte" <rdia...@gmail.com> wrote:
>>>
>>>>
>>>> Dear All,
>>>>
>>>> I am considering rewriting the vignette of one BioC package I maintain as
>>>> Rmd (it is currently Rnw). But I would like that the entry under
>>>> "Documentation" contain a PDF of the vignette; it can ideally also contain
>>>> the HTML version too, but I do not want it to not have the PDF[1].
>>>>
>>>>
>>>> I know I can add entries to the document header such as
>>>>
>>>> output:
>>>> BiocStyle::pdf_document:
>>>> toc: true
>>>> BiocStyle::html_document:
>>>> toc: true
>>>>
>>>>
>>>> that will, when run locally via "render('file.Rmd', output_format =
>>>> 'all')", produce both formats.
>>>>
>>>>
>>>>
>>>> I've googled around, but I am not sure about:
>>>>
>>>> 1. If I have both output formats specified in the document header, will the
>>>> BioC page of the package actually show both the PDF and the HTML of the
>>>> vignette?
>>>>
>>>>
>>>> 2. Is it OK (in conforming with BioC policies, sensible[1], whatever) to
>>>> even try/want this? My reading of the doc for the BiocStyle
>>>> (https://www.bioconductor.org/packages/devel/bioc/vignettes/
>>>> BiocStyle/inst/doc/HtmlStyle.html)
>>>> seems to suggest that the "natural" thing for Rmd vignettes is to be
>>>> rendered as HTML, but I have not seen that producing PDF is discouraged
>>>> explicitly.
>>>>
>>>>
>>>> Best,
>>>>
>>>>
>>>> R.
>>>>
>>>>
>>>> [1] Why do I want to get a PDF if I am using Rmd? I want a PDF because this
>>>> is a fairly long document that some users want to be able to print. I want
>>>> HTML because some users prefer HTML and because I'd like to also place the
>>>> vignette as HTML in Github Pages. I think that the only way to accomplish
>>>> both is to use Rmd (not Rnw, even if I really, really, prefer LaTeX :-).
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Ramon Diaz-Uriarte
>>>> Department of Biochemistry, Lab B-25
>>>> Facultad de Medicina
>>>> Universidad Autónoma de Madrid
>>>> Arzobispo Morcillo, 4
>>>> 28029 Madrid
>>>> Spain
>>>>
>>>> Phone: +34-91-497-2412
>>>>
>>>> Email: rdia...@gmail.com
>>>> ramon.d...@iib.uam.es
>>>>
>>>> http://ligarto.org/rdiaz
>>>>
>>>> _______________________________________________
>>>> Bioc-devel@r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>>
>> This email message may contain legally privileged and/or...{{dropped:2}}
>>
>> _______________________________________________
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdia...@gmail.com
ramon.d...@iib.uam.es
http://ligarto.org/rdiaz
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
