[R] Warning message: cannot create HTML package index

Peter Dalgaard P.Dalgaard at biostat.ku.dk
Fri Jul 6 12:49:21 CEST 2007

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)
which has a link to

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

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

   O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)                  FAX: (+45) 35327907

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