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? This
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 ëUsingRí 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 ëUsingRí 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
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