On Wed, Nov 21, 2012 at 2:49 PM, Hervé Pagès <hpages@fhcrc.org> wrote:

> On 11/21/2012 01:33 PM, Michael Lawrence wrote:
>
>> On Wed, Nov 21, 2012 at 11:25 AM, Martin Morgan <mtmorgan@fhcrc.org>
>> wrote:
>>
>>  On 11/21/2012 09:08 AM, Michael Lawrence wrote:
>>>
>>>  This may already be documented somewhere, but do the package pages on
>>>> the
>>>> bioc website link to any file present in inst/doc? Or does it only work
>>>> for
>>>> PDF vignettes? It would be neat if people could produce vignettes in any
>>>> format and have them linked from the package pages.
>>>>
>>>> This relates to Sean's idea of having wiki-like webs of documentation.
>>>> In
>>>> theory, if HTML documents were included, they could link to other HTML
>>>> documents embedded in other packages. Ideally, there would also be
>>>> "meta"
>>>> documents that describe high-level concepts and bridge packages.
>>>>
>>>> But I think at least linking to HTML documents in inst/doc would be an
>>>> easy
>>>> and useful first step, if it isn't supported already.
>>>>
>>>>
>>> Hi Michael --
>>>
>>> That's an interesting idea. There are some obstacles. For instance, a
>>> file
>>> inst/doc/index.html can already be installed and accessible through R's
>>> help system (help.start(), navigate to package page, then 'Overview of
>>> user
>>> guides and package vignettes'; an example is in RGalaxy). There's then a
>>> conflict between url's that are relative vs. fully specified.
>>>
>>>
>>>  I must be missing something. I would assume that any user written HTML
>> would want to use relative paths (for local links) and that those would
>> work the same whether on the bioc website or the package installation, as
>> long as everything falls under inst/doc. At least in the RGalaxy example,
>> those relative URLs should work just fine, as long as inst/doc is copied
>> in
>> full to some directory on the bioc website.
>>
>
> That would work just fine for cross-linking of documents within the
> same package. My understanding of the small technical obstacle with
> inter-package links is that at installation time everything under
> MyPackage/inst/doc/ ends up under MyPackage/doc/ so in their vignettes
> people would need to use relative URLs of the form
>
>   ../../OtherPackage/doc/**OtherPackageVignette.html
>
> which I believe might conflict with the layout currently in use on the
> website. Certainly not something that could not be addressed though...
>
>
Sure, we would just need a convention for cross-package linking. The above
would not work anyway locally, because packages need not all be in the same
lib path. When viewing the HTML locally, my understanding is that it is
using the R internal web server. We could in theory hook into that to
properly resolve package names to paths.


> I wonder it wouldn't be worth pursuing the same goal for all the man
> pages of all BioC packages. Would be great to be able to navigate them
> on line (like we can do locally with help.start(), except that I can
> only browse what is already installed of course).
>
>
Sure, good idea.


> Cheers,
> H.
>
>
>
>>
>>  Maybe there are ways to exploit R's help system more creatively? Or the
>>> project could adopt a convention, 'files in inst/doc/bioc are linked from
>>> the landing page'?
>>>
>>> Martin & Dan
>>>
>>>
>>>  Michael
>>>>
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>>>>
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>>>>
>>>>
>>>>
>>> --
>>> Computational Biology / Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N.
>>> PO Box 19024 Seattle, WA 98109
>>>
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>>>
>>>
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>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
>
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
>
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