user library help functionality (packages.html)

This helps a lot.  I have options(htmlhelp=TRUE) and  
options(chmhelp=FALSE) (else problems).  Now, ?, help(), and  
help.search() seem to work well.  But, help.start() appears restricted  
to packages in the site library.  I see, in the Help/FAQ on R for  
Windows/ Sections 4.3 and 4.4, that I cannot expect more from  
help.start() unless I have write permission to $RHOME/library, which I  
do not (package does have a CONTENTS file however).  I assume that, if  
I want my students to have this functionality, they, too, would need  
write access to $RHOME/library, correct?  But, this does not seem a  
wise thing to give.  Am I missing something here, barring permission  
changes, that would allow help.search() to see user libraries?  

would be ideal, but your suggestions seems to give us nice help  
functionality, and I think we can implement an R installation campus- 
wide without the full functionality of help.seach().  Thanks very much.

Jarrett


R Session:

R version 2.7.0 (2008-04-22)
...snip...

 > personalLib<- .libPaths()[1]; personalLib

[1] "H:\\Desktop\\RFiles\\Library"

 > getOption("htmlhelp")

[1] TRUE

 > getOption("chmhelp")

[1] FALSE

 > install.packages("UsingR",

+ lib=personalLib,
+ depend=TRUE)
trying URL 'http://streaming.stat.iastate.edu/CRAN/bin/windows/contrib/2.7/UsingR_0.1-10.zip'
Content type 'application/zip' length 1433201 bytes (1.4 Mb)
opened URL
downloaded 1.4 Mb

package 'UsingR' successfully unpacked and MD5 sums checked

The downloaded packages are in
         C:\Temp\RtmpQr4t3E\downloaded_packages
updating HTML package descriptions
Warning message:
In file.create(f.tg) :
   cannot create file 'C:\PROGRA~1\R\R-27~1.0/doc/html/packages.html',  
reason 'Permission denied'  ## PERMISSION PROBLEM

 > library("UsingR")

Warning message:
package 'UsingR' was built under R version 2.7.2

 > help("UsingR") ## works!

Help for ?UsingR? is shown in the browser

 > help.start() ## restricted to site library

updating HTML package listing
updating HTML search index
fixing URLs in non-standard libraries
If nothing happens, you should open 'C:\PROGRA~1\R\R-27~1.0\doc\html 
\index.html' yourself
Warning message:
In file.create(f.tg) :
   cannot create file 'C:\PROGRA~1\R\R-27~1.0/doc/html/packages.html',  
reason 'Permission denied' ## SAME PERMISSION PROBLEM

 > help.search("UsingR") ## works!
 > ?UsingR ## works!

Help for ?UsingR? is shown in the browser

 > q()

On Jan 15, 2009, at 11:42 AM, Duncan Murdoch wrote:

On 1/15/2009 12:50 PM, Jarrett Barber wrote:

Here's another help file question.
Some context: University setting wherein R is installed for   
availability to students and course instructors across campus in   
various PC labs.  Windows Vista environment.
Goal: To maximize flexibility and functionality of installing add- 
on  packages and associated help files among different users,  
while  avoiding conflicts across different user libraries.  (I  
could have my  difficult-to-access sysadmin install _all_  
libraries, but this seems  wasteful, and would seem to present  
problems when my colleague or I  want to update a package or  
install a newly available package but do  not have time to wait a  
week or two for our sysadmin.)
Problem (?): As a course instructor, I want flexibility to install  
add- on libraries to a user (not site) library, and I don't want to  
step on  my colleagues' toes (or vice-versa) when it comes to add- 
on packages  and associated help files for use in classes.  I have  
no problem  installing add-on packages to a user library, with one  
exception: I do  not have permission to update the file $RHOME/doc/ 
html/packages.html,  as evidenced by a permission error upon  
installing a package to a user  library using update.packages (not  
to the default site library, which  is also restricted).  The  
installed add-on packages work fine, with  the exception of some of  
the help functionality.  I find myself having  to use browseURL()  
to point to the html files in the package's file  structure.  I  
cannot expect the average student (or senior colleague)  to  
tolerate this situation.

A simpler way to get to the HTML man pages is to run

options(htmlhelp=TRUE)

and then the regular ?topic or help("topic") will find the HTML help  
pages in your local library.

I'm thinking that I simply need to have my sysadmin give me and my   
colleagues (all users who want to install add-ons packages?)   
permission to read/write packages.html, and the problem will go  
away.   But, before I ask my sysadmin to give permission, I want to  
know, does  this create another problem?  For example, my colleague  
creates a  library for STAT3000BC, which, I assume, will modify  
packages.html  (assuming my sysadmin gives permission), then I  
create a library for  STAT2010, which also modifies packages.html.   
See my concern?  Does R  somehow allow harmonious help  
functionality in such cases (by, for  example, maintaining separate  
copies of packages.html for different  users)?

You will likely have strange problems if you do that.  The doc/html/ 
packages.html file is intended to talk about what is available to  
everyone; I suspect in your scenario, it would be updated to show  
your packages (but not your colleague's) whenever you added one, and  
then updated to show your colleague's packages (but not yours) when  
he added one, and would almost never be right for both of you.

The good news is that it looks as though sometime this year we will  
make quite substantial changes to the way the help system is stored,  
so a lot of things like packages.html could be generated on the fly.

Duncan Murdoch