R devel - Jun 2004 - Can´t start help and update on Mac (PR#6920

--Apple-Mail-1--963012407
Content-Transfer-Encoding: 7bit
Content-Type: text/plain;
	charset=US-ASCII;
	format=flowed

Hi,

I get exactly the same error message as in report no 6920. Furthermore, 
starting "update Bioconducter" the following message appears (running 
Mac OS X 10.3.4 (7H63)) :

 > {library(reposTools);update.packages2(getAllDeps=TRUE)}

Synching your local package management information ...
Packages which have been added/updated:
	sm
	sma
	wavethresh
	


	Note: reposTools can not access 
/Library/Frameworks/R.framework/Resources/library.
	This will not affect your R session unless you wish
	to install/update/remove packages from this directory

Note: argument `lib' is missing: using /Users/admin/Library/R/library
  Note: argument `lib' is missing: using 
/Library/Frameworks/R.framework/Resources/library
  Note: argument `lib' is missing: using 
/tmp/RtmpKEgaWQ/tempLibs/file3ab50c2a

Synching your local package management information ...

	Note: reposTools can not access 
/Library/Frameworks/R.framework/Resources/library.
	This will not affect your R session unless you wish
	to install/update/remove packages from this directory

Error in lapply(locLibList, Package) : Object "locLibList" not found

 >


Sincerely

           Hans Kestler
--Apple-Mail-1--963012407
Content-Transfer-Encoding: 7bit
Content-Type: text/enriched;
	charset=US-ASCII

Hi,


I get exactly the same error message as in report no 6920.
Furthermore, starting "update Bioconducter" the following message
appears
(<fontfamily><param>Lucida
Grande</param><x-tad-smaller>running Mac OS
X 10.3.4 (7H63)</x-tad-smaller></fontfamily>) :


<fixed><color><param>0000,0000,FFFF</param><x-tad-bigger>>
{library(reposTools);update.packages2(getAllDeps=TRUE)}


Synching your local package management information ...

Packages which have been added/updated:

	sm

	sma

	wavethresh

	



	Note: reposTools can not access
/Library/Frameworks/R.framework/Resources/library.

	This will not affect your R session unless you wish 

	to install/update/remove packages from this directory

 

Note: argument `lib' is missing: using /Users/admin/Library/R/library 

 Note: argument `lib' is missing: using
/Library/Frameworks/R.framework/Resources/library 

 Note: argument `lib' is missing: using
/tmp/RtmpKEgaWQ/tempLibs/file3ab50c2a 


Synching your local package management information ...


	Note: reposTools can not access
/Library/Frameworks/R.framework/Resources/library.

	This will not affect your R session unless you wish 

	to install/update/remove packages from this directory

 

Error in lapply(locLibList, Package) : Object "locLibList" not found

> 


</x-tad-bigger></color><color><param>0000,0000,0000</param><x-tad-bigger>Sincerely


          Hans Kestler</x-tad-bigger></color></fixed>
--Apple-Mail-1--963012407--

reposTools is part of Bioconductor not R.  Please use the correct bug 
repository.

Note that PR#6920 does not mention any `error message' whatsoever (nor
does it claim to): the message quoted

help.start()
Making links in per-session dir ...
If /usr/bin/open is already running, it is *not* restarted, and you 
must switch to its
     window.
Otherwise, be patient ...

is the standard informational message.  We need to know what the error 
actually is.  If no browser window opens, then does it help to have one 
open already?  (Was true of Netscape 7.0.)  Does setting a more standard 
browser (e.g. Mozilla) solve this ....

On Thu, 10 Jun 2004 kestler@onlinehome.de wrote:
> 
> --Apple-Mail-1--963012407
> Content-Transfer-Encoding: 7bit
> Content-Type: text/plain;
> 	charset=US-ASCII;
> 	format=flowed
> 
> Hi,
> 
> I get exactly the same error message as in report no 6920. Furthermore, 
> starting "update Bioconducter" the following message appears
(running
> Mac OS X 10.3.4 (7H63)) :
> 
>  > {library(reposTools);update.packages2(getAllDeps=TRUE)}
> 
> Synching your local package management information ...
> Packages which have been added/updated:
> 	sm
> 	sma
> 	wavethresh
> 	
> 
> 
> 	Note: reposTools can not access 
> /Library/Frameworks/R.framework/Resources/library.
> 	This will not affect your R session unless you wish
> 	to install/update/remove packages from this directory
> 
> Note: argument `lib' is missing: using /Users/admin/Library/R/library
>   Note: argument `lib' is missing: using 
> /Library/Frameworks/R.framework/Resources/library
>   Note: argument `lib' is missing: using 
> /tmp/RtmpKEgaWQ/tempLibs/file3ab50c2a
> 
> Synching your local package management information ...
> 
> 	Note: reposTools can not access 
> /Library/Frameworks/R.framework/Resources/library.
> 	This will not affect your R session unless you wish
> 	to install/update/remove packages from this directory
> 
> Error in lapply(locLibList, Package) : Object "locLibList" not
found
> 
>  >
> 
> 
> Sincerely
> 
>            Hans Kestler

-- 
Brian D. Ripley,                  ripley@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595