[Bioc-devel] non-pdf documents linked from package pages?

Hervé Pagès hpages at fhcrc.org
Wed Nov 21 23:49:53 CET 2012

On 11/21/2012 01:33 PM, Michael Lawrence wrote:
> On Wed, Nov 21, 2012 at 11:25 AM, Martin Morgan <mtmorgan at 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


which I believe might conflict with the layout currently in use on the
website. Certainly not something that could not be addressed though...

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).


>> 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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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
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E-mail: hpages at fhcrc.org
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