Relative URLs

[ms609]

New CRAN test reports:

Version: 2.11.1
Check: relative paths in package URLs
Result: NOTE 
  Found the following (possibly) invalid URL:
    URL: ../reference/index.html
      From: inst/doc/using-distances.html
Flavors: [r-devel-linux-x86_64-debian-clang](https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/TreeDist-00check.html), [r-devel-linux-x86_64-debian-gcc](https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/TreeDist-00check.html)

Explanatory message from KH reads:

Specifically, please see the NOTEs about possibly invalid URLs in the
"relative paths in package URLs" check for the debian r-devel flavors.

This is a recently added check which tests whether URLs using relative
paths (and no scheme) in Rd files or HTML vignette outputs work in
dynamic help.

In general, packages can link from their help pages to their vignette
outputs using

../doc/FOO.html
../doc/FOO.pdf

and from their vignette outputs to their help files or topics using,
respectively,

../html/FILE.html
../help/TOPIC

(We have recently also allowed for ../articles as synonym for ../doc and
for ../reference as synonym for ../html.)

A package can also link to vignette outputs and help files/topics in
another package PKG by replacing ../ by ../PKG/.

There are a few other relative paths which work in dynamic help, but are
best avoided, as they cannot easily be made to work for the CRAN package
web pages.

Can you please take a look at the new NOTEs and fix "as necessary"?

If you use a relative path you think should work or be made to work,
please let me know.

(E.g., a few packages use ../reference/index.html which I guess should
be ../reference/00Index.html, but may be intended differently?)