On 11/21/2012 01:33 PM, Michael Lawrence wrote:
On Wed, Nov 21, 2012 at 11:25 AM, Martin Morgan <mtmor...@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...
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).
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
[[alternative HTML version deleted]]
______________________________**_________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/**listinfo/bioc-devel<https://stat.ethz.ch/mailman/listinfo/bioc-devel>
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
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: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
