[R-SIG-Mac] Can't get help.start() to work.

[Simon Urbanek]

Rolf,

On Oct 28, 2009, at 23:39 , Rolf Turner wrote:

>
> On 29/10/2009, at 2:39 PM, Duncan Murdoch wrote:
>
>> On 28/10/2009 9:04 PM, Rolf Turner wrote:
>>> Under my newly installed version of R, 2.10.0, help.start() refuses
>>> to perform.  When I issue the command I get a ``Host is  
>>> unreachable''
>>> message from the browser (which is Firefox, version 3.5.3).
>>>
>>> I have seen things about funnies with help under 2.10.0 but have
>>> not properly comprehended them.  I am not sure if they apply to my
>>> situation.  I did a bit of scrounging through recent postings to
>>> R-help and could not find anything relevant. Can someone tell me
>>> ***in monosyllables*** ( :-) ) how to get help.start() to work?
>>>
>>> Session info:
>>>
>>>> R version 2.10.0 Patched (2009-10-27 r50222)
>>>> i386-apple-darwin8.11.1
>>>>
>>>> locale:
>>>> [1] C
>>>>
>>>> attached base packages:
>>>> [1] datasets  utils     stats     graphics  grDevices methods    
>>>> base
>>>>
>>>> other attached packages:
>>>> [1] misc_0.0-11    fortunes_1.3-6 MASS_7.3-3
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] tools_2.10.0
>>>
>>> I have attached, in pdf form, a screen shot of the message I get
>>> in the Firefox window when help.start() fails.
>>
>> The problem appears to be with "WebMarshal Proxy".  I don't know if  
>> you
>> have any control over this, or it comes from your IT department,  
>> but you
>> need to tell it to let Firefox connect to R on your own machine  
>> (address
>> 127.0.0.1) if you want help.start() to work.  If that requires you to
>> set a particular port number (or range) for R to use, see the
>> ?tools::startDynamicHelp page for details.
>
> 	This did not/does not happen with R version 2.9.2.  Why has
> 	version 2.10.0 introduced a difficulty?
>>
>> You may find that the GUI works better.  It doesn't use Firefox, it  
>> has
>> its own built in browser, and it's conceivable that it will avoid  
>> going
>> through the proxy.
>
> Yes, the GUI works in respect of providing html help.  But
>
> 	(a) I ***HATE*** using the GUI.
>
> 	(b) Funny things happen when I try loading spatstat from the GUI.
>
> 	If I click on Packages & Data --> Package Manager, I get an error:
>
>> Error in package.manager(is.loaded, pkgs, pkgs.desc, pkgs.url) :
>>  invalid arguments (length mismatch)
>> In addition: Warning messages:
>> 1: In .find.package(pkgs) : there is no package called 'BACCO'
>> 2: In .find.package(pkgs) : there is no package called 'forecasting'
>
>
> 	There ***are*** packages BACCO and forecasting in my local
> 	library (~/Rlib).  But ne'er mind.
>
> 	So I try
>
> 	library(spatstat)
>
> 	from the command line (in the window opened by the GUI).  I get an  
> error:
>
>> Loading required package: mgcv
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>  unable to load shared library '/Users/rturner/Rlib/lattice/libs/ 
>> i386/lattice.so':
>>  dlopen(/Users/rturner/Rlib/lattice/libs/i386/lattice.so, 6):  
>> Library not loaded: /Library/Frameworks/R.framework/Versions/2.7/ 
>> Resources/lib/libR.dylib

note the version 2.7 there - you have apparently old packages for a  
different version of R on your .libPaths() -- bad thing.


>>  Referenced from: /Users/rturner/Rlib/lattice/libs/i386/lattice.so
>>  Reason: image not found
>> In addition: Warning message:
>> package 'spatstat' was built under R version 2.9.2 and help may not  
>> work correctly
>> Error: package 'mgcv' could not be loaded
>
> 	However if I abandon the (expletive deleted) GUI, start R from the  
> command
> 	line and then load spatstat, all is well.  (Modulo some warnings  
> about packages
> 	being built under earlier versions of R whence the help might not  
> work correctly.
> 	Which it doesn't anyway.)
>

Packages built for earlier versions of R usually don't work, period.  
If you get lucky, they might under certain circumstances, but you  
should always assume that they don't.


> 	So why should mgcv load when R is started from the command line,  
> but not
> 	when it is started from the GUI?
>

Check your .libPaths() - I bet they are different and you have  
outdated packages in one of them. If you wonder why, check your  
preferences.


> 	This is getting ridiculous.  Everything I try engenders another  
> error and
> 	another fiasco.  Things have become too complex and intricate.   
> IMHO too
> 	much effort has been expended on implementing gee-whiz facilities  
> for the
> 	super-clever or GUI facilities for the retarded at the expense of  
> simple
> 	usability for the ordinary middle of the road user.
>

I suspect this is all rather due to the customization and chaos  
created by the user ;) - the GUI actually tries to prevent such things  
by using separate library directories for each R version by default,  
but if you override that with your settings (especially using one  
global library), you can mess up things - but that's true in R in  
general, not really related to GUIs.

Cheers,
Simon