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Help.start() issues

7 messages · Paul Rathouz, Simon Urbanek, George W. Gilchrist +2 more

Original
George W. Gilchrist
# 
Sorry to bother folks, but what browsers are known to work for help.start()
on OS X (just installed Panther...)? I use Safari for most things, but it
does not seem to work for /usr/local/lib/R/doc/html/index.html. Something
about the Java script involved in searching does not run correctly. I have
the same problem with Netscape 7.1. The last "success" I had was with
Netscape 7.0. Does anyone have a better suggestion? Thanks, as always.

Cheers, George

==================================================================
George W. Gilchrist                        Email #1: gwgilc@wm.edu
Department of Biology, Box 8795          Email #2: kitesci@cox.net
College of William & Mary                    Phone: (757) 221-7751
Williamsburg, VA 23187-8795                    Fax: (757) 221-6483
http://gwgilc.people.wm.edu/
Paul Rathouz
# 
George --

I have heard that in order to get this to work correctly, you have to use
an old browser running under darwin / x11.

Here is my work-around:

- I use safari as my default, so I go through help.start() to launch it,
and then click on "packages" and then to the command i am interested in.

- if I want to do a search, then I use the help.search() command to get a
list of possible commands, and then I just look in those commands using
safari as my browser.

not perfect, but functional . . . the help.search() command is key.

-- pr
On Fri, 14 Nov 2003, George W. Gilchrist wrote:

            

      
      
      
    

        

      
      
    

        
==========================================================================
Paul Rathouz, Asst. Professor        ph   773-834-1970
Dept. of Health Studies, Rm. W-264   fax  773-702-1979
University of Chicago                prathouz@health.bsd.uchicago.edu
5841 S. Maryland Ave. MC 2007
Chicago, IL  60637

  
  


  


      

    

    
2 days later

    

      
      

        


  

        

      Simon Urbanek
    

    

      
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On Nov 14, 2003, at 3:25 PM, George W. Gilchrist wrote:

        

            

      
      
      
    

        
I'm using Camino and it works perfectly out of the box ... (I just set 
it up in Apple's Internet Preferences).

Cheers,
Simon

---
Simon Urbanek
Department of computer oriented statistics and data analysis
University of Augsburg
Universit?tsstr. 14
86135 Augsburg
Germany

Tel: +49-821-598-2236
Fax: +49-821-598-2200

Simon.Urbanek@Math.Uni-Augsburg.de
http://simon.urbanek.info

  
  


  


      

    

    

      
      

        


  

        

      George W. Gilchrist
    

    

      
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Simon,

I'm just not living right... Camino loads up fine, but I cannot search for
anything on the R help page. I'm not sure what the problem is. Several folks
have reported this in the past with the last solution I found to be to use
Netscape 7.0 or earlier. Yet I see folks talking about using Safari or
Camino successfully, but it does not happen for me. Thanks for your
comments, though!

Cheers, George



On 11/17/03 4:58 AM, "Simon Urbanek" <Simon.Urbanek@math.uni-augsburg.de>
wrote:

            

      
      
      
    

        
==================================================================
George W. Gilchrist                        Email #1: gwgilc@wm.edu
Department of Biology, Box 8795          Email #2: kitesci@cox.net
College of William & Mary                    Phone: (757) 221-7751
Williamsburg, VA 23187-8795                    Fax: (757) 221-6483
http://gwgilc.people.wm.edu/

  
  


  


      

    

    

      
      

        


  

        

      stefano iacus
    

    

      
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George,
I don't think you'll be successfull to doing search from the browser 
(any apart old versions of Netscape apparently).

If you cannot even start safari from RAqua that hte problem comes from 
the libiconv library which is in your /usr/local/lib.
You should have a llok at the Console application when trying to do 
this, it should report an error on that.
Pnather has a new version of libiconv library which is backward 
compatible. Have a look at the RAqua faq 
http://cran.r-project.org/bin/macosx/RAqua-FAQ.html

You can try to use the help.search from inside R which has a menu item 
in the Hepl menu.
If you don't like the internal viwer but you prefer a browser, just set 
the option

options("htmlhelp"=TRUE)

and it will open html help files

stefano


On Luned?, nov 17, 2003, at 18:20 Europe/Rome, George W. Gilchrist 
wrote:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
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On Nov 17, 2003, at 7:03 PM, Stefano Iacus wrote:

        

            

      
      
      
    

        
There is one more pitfall that could be mentioned: R still includes  
/usr/X11R6/lib in DYLD_LIBRARY_PATH, which breaks a lot of things,  
beside R packages also any applications that are launched from R,  
including Camino. You will probably want to include something like this  
in one of the startup files (or the shell equivalent if desired):

Sys.putenv("DYLD_LIBRARY_PATH"=sub("/usr/X11R6/ 
lib","",Sys.getenv("DYLD_LIBRARY_PATH")))

But Stefano is right that you're not likely to get the search to work.  
A brief debugging reveals what I suspected:

java.security.AccessControlException: access denied  
(java.io.FilePermission  read)
	at  
java.security.AccessControlContext.checkPermission(AccessControlContext. 
java:270)
	at  
java.security.AccessController.checkPermission(AccessController.java: 
401)
	at java.lang.SecurityManager.checkPermission(SecurityManager.java:542)
	at java.lang.SecurityManager.checkRead(SecurityManager.java:887)
	at java.io.File.exists(File.java:677)
	at sun.net.www.protocol.file.Handler.openConnection(Handler.java:62)
	at java.net.URL.openConnection(URL.java:943)
[...]

It is the old security issue of applets. I've (briefly) seen a lot of  
discussions about this, anyone interested may "google" for it, but  
solutions involve signing the class/jar files and similar approaches.  
Another possibility would be to hard-code the index into the source but  
then it would have to be re-compiled on update etc... I never really  
dealt with this (I used the hard-coded solution or sockets), so it's  
just a guess ;).

BTW: Who is the author of the applet code and has the sources? It's  
hard to debug it when you don't have the source code :P

Cheers,
Simon

---
Simon Urbanek
Department of computer oriented statistics and data analysis
Universit?tsstr. 14
86135 Augsburg
Germany

Tel: +49-821-598-2236
Fax: +49-821-598-2280

Simon.Urbanek@Math.Uni-Augsburg.de
http://simon.urbanek.info

  
  


  


      

    

    

      
      

        


  

        

      Martin Maechler
    

    

      
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Simon> On Nov 17, 2003, at 7:03 PM, Stefano Iacus wrote:

        
>> George,
    >> I don't think you'll be successfull to doing search from the browser  
    >> (any apart old versions of Netscape apparently).
    >> 
    >> If you cannot even start safari from RAqua that hte problem comes from  
    >> the libiconv library which is in your /usr/local/lib.

    Simon> BTW: Who is the author of the applet code and has the sources? It's  
    Simon> hard to debug it when you don't have the source code :P

Most of the programming originates from Thomas Baier AFAIK;
formally, the author now is R core and the source is in R's source :-) 
inside the  doc/html/search/*.java files.

Regards,
Martin