[R] Warning message: cannot create HTML package index

[Prof Brian Ripley]

On Fri, 6 Jul 2007, Peter Dalgaard wrote:

> Leo wrote:
>> On 06/07/2007, Prof Brian Ripley wrote:
>>
>>> On Fri, 6 Jul 2007, Leo wrote:
>>>
>>>
>>>> I have set R_LIBS=~/R_lib as I don't have root access.
>>>>
>>>> The following message shown up every time after installing a package:
>>>>
>>>>  ......
>>>>  The downloaded packages are in
>>>>  	/tmp/RtmpBoIPoz/downloaded_packages
>>>>  Warning message:
>>>>  cannot create HTML package index in: tools:::unix.packages.html(.Library)
>>>>
>>>> Any ideas?
>>>>
>>> It is a correct warning.  What is the problem with being warned?
>>>
>>> R tries to maintain an HTML page of installed packages, but you don't have
>>> permission to update it.
>>>
>>
>> Where is that HTML page located on a GNU/Linux system?
>>
>> Is it possible to maintain a user HTML page of installed packages?
>>
>> Thanks,
>>
> This confuses me a bit too. I had gotten used to the warning without
> thinking about it. It tries to update $RHOME/doc/html/packages.html,
> which starts like this:
>
> .....
> <p><h3>Packages in the standard library</h3>
> .....
>
> However, if I run help.start, I get
>
>> help.start()
> Making links in per-session dir ...
> If 'firefox' is already running, it is *not* restarted, and you must
>    switch to its window.
> Otherwise, be patient ...
>
> and then it opens (say)
>  file:///tmp/RtmpXyp5Cg/.R/doc/html/index.html
> which has a link to
>  file:///tmp/RtmpXyp5Cg/.R/doc/html/packages.html
>
> which looks like this
>
> ....
> <p><h3>Packages in /home/bs/pd/Rlibrary</h3>
> ....
> <p><h3>Packages in /usr/lib64/R/library</h3>
>
> I.e. it is autogenerated by help.start and doesn't even look at the file
> in $RHOME. So what puzzles me is
>
> (a) why we maintain $RHOME/doc/html/packages.html at all
>
> One argument could be that this is browseable for everyone on a system,
> even without starting R. But then

Some front-end GUIs use it (or used to use it).

> (b) why do we even try updating it when packages are installed in a
> private location?

We don't know that.  Given the use of symbolic links, it is not clear 
which libraries are private and which are links to .Library.  However, we 
could be less cautious about this, and I've altered the code to update 
only if the path matches .Library exactly.

-- 
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