Whoops! Yes, my last "help.search()" should have been
"help.start()". Thanks again. -- Jarrett
On Jan 15, 2009, at 1:27 PM, Duncan Murdoch wrote:
On 1/15/2009 3:17 PM, Jarrett Barber wrote:
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?
You mean help.start() here, don't you? help.search() does see
everything in the libraries listed in .libPaths().
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.
As far as I know on Windows there's currently no way to get
help.start() to go to a personalized page. The stuff that it refers
to all lives in RHOME/doc/html, and many of the links in the files
it works with assume that they are installed in the same hierarchy.
I'm not sure if things are different on Unix, where we use soft
links to make all the package directories appear to be under one
parent.
Duncan Murdoch
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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