R devel - Oct 2009 - linking to package directories broken in R >= 2.10 beta

Dear R developers,

some of our packages come with additional programming examples in a 
directory called "/examples" which is created from
"/inst/examples".

This directory is linked from the docs (e.g. in inst/doc/index.html):

<dl>
<dt><a href="../examples/">examples</a>:
<dd>Source code of examples
</dl>

Given, that we have a package "foo" this is resolved to:

file:///C:/Programme/R/R-2.9.2/library/foo/examples/

with R <= 2.9.2. With R 2.10 beta (R-beta_2009-10-16_r50118.tar.gz) and 
R-devel (svn rev. 50118) we get:

http://127.0.0.1:26383/library/foo/examples/

This is fine, but in contrast to older versions (<= 2.9.2) no automatic 
index is created for the linked directory, so we now get:

"URL /library/foo/examples/ was not found"

bu linking to *individual files* (e.g. examples/example.R) works as 
expected. We can, of course, add manually maintained index files but I 
would much prefer if a default index would be created for the directory 
if no index.html is found.

I very much enjoy the new help system and would be even more happy if 
that issue could be fixed.

Thomas Petzoldt


PS: A minimal reproducible example (foo_1.0.tar.gz) can be provided by 
mail if required.

-- 
Thomas Petzoldt
Technische Universitaet Dresden
Institut fuer Hydrobiologie        thomas.petzoldt at tu-dresden.de
01062 Dresden                      http://tu-dresden.de/hydrobiologie/
GERMANY

Thomas Petzoldt wrote:
> Dear R developers,
>
> some of our packages come with additional programming examples in a 
> directory called "/examples" which is created from
"/inst/examples".
>
> This directory is linked from the docs (e.g. in inst/doc/index.html):
>
> <dl>
> <dt><a href="../examples/">examples</a>:
> <dd>Source code of examples
> </dl>
>
> Given, that we have a package "foo" this is resolved to:
>
> file:///C:/Programme/R/R-2.9.2/library/foo/examples/
>
> with R <= 2.9.2. With R 2.10 beta (R-beta_2009-10-16_r50118.tar.gz) and 
> R-devel (svn rev. 50118) we get:
>
> http://127.0.0.1:26383/library/foo/examples/
>
> This is fine, but in contrast to older versions (<= 2.9.2) no automatic 
> index is created for the linked directory, so we now get:
>
> "URL /library/foo/examples/ was not found"
>
> bu linking to *individual files* (e.g. examples/example.R) works as 
> expected. We can, of course, add manually maintained index files but I 
> would much prefer if a default index would be created for the directory 
> if no index.html is found.
>   
By "index" in R <= 2.9.2, you mean the default directory listing 
produced by the web server, rather than something produced by R, right?  
The R server does that now if the directory is named "doc", but not
for
an arbitrary path.  We are concerned about security:  any user on your 
system who can guess your port number can access your help system, so we 
want to be sure that such users can't access private files.

Duncan Murdoch
> I very much enjoy the new help system and would be even more happy if 
> that issue could be fixed.
>
> Thomas Petzoldt
>
>
> PS: A minimal reproducible example (foo_1.0.tar.gz) can be provided by 
> mail if required.
>
>

When you linked to ../examples/ R was not involved, and what you are 
seeing is what your browser did with a file:// url.  Most browsers 
will support a wide range of file types, and list directories: but 
that is not something that was ever (AFAICS) documented to work.

The 'issue' is your expectations when creating your own 
inst/doc/index.html.  The only relative links that are supported by 
the help system are to R package help topics and files, to 
documentation under R.home("doc") and a limited set of files in a 
package's 'doc' directory to support its use for vignettes,
including
the ability to list 'doc' itself (if requested in a particular way).

If links to files under <pkg>/example worked, it was a bug. Because of 
security concerns over traffic snooping, what you can see through the 
dynamic help system is intentionally very limited.  In fact I suspect 
they worked for you only because

(i) you installed into .Library
(ii) you had a file for which text/plain worked (and that is because 
files that might be in a vignette directory have been checked)..
(iii) you fell into a code branch marked '# should not get here' in 
pre-2.10.0 (but absent in R-devel).

The good news is that if you refer to files under the installed 'doc' 
directory this should work -- subdirectory listings work now in 
R-devel and will probably be ported to 2.10.0 before release.


On Sat, 17 Oct 2009, Thomas Petzoldt wrote:
> Dear R developers,
>
> some of our packages come with additional programming examples in a
directory
> called "/examples" which is created from
"/inst/examples".
>
> This directory is linked from the docs (e.g. in inst/doc/index.html):
>
> <dl>
> <dt><a href="../examples/">examples</a>:
> <dd>Source code of examples
> </dl>
>
> Given, that we have a package "foo" this is resolved to:
>
> file:///C:/Programme/R/R-2.9.2/library/foo/examples/
>
> with R <= 2.9.2. With R 2.10 beta (R-beta_2009-10-16_r50118.tar.gz) and 
> R-devel (svn rev. 50118) we get:
>
> http://127.0.0.1:26383/library/foo/examples/
>
> This is fine, but in contrast to older versions (<= 2.9.2) no automatic
index
> is created for the linked directory, so we now get:
>
> "URL /library/foo/examples/ was not found"
>
> bu linking to *individual files* (e.g. examples/example.R) works as
expected.
> We can, of course, add manually maintained index files but I would much 
> prefer if a default index would be created for the directory if no
index.html
> is found.
>
> I very much enjoy the new help system and would be even more happy if that 
> issue could be fixed.
>
> Thomas Petzoldt
>
>
> PS: A minimal reproducible example (foo_1.0.tar.gz) can be provided by mail
> if required.
>
> -- 
> Thomas Petzoldt
> Technische Universitaet Dresden
> Institut fuer Hydrobiologie        thomas.petzoldt at tu-dresden.de
> 01062 Dresden                      http://tu-dresden.de/hydrobiologie/
> GERMANY
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595