[R] Remove site path from .libPaths

[Duncan Murdoch]

On 13-02-15 9:28 AM, Rainer M Krug wrote:
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> Hi
>
> I am sure I am missing something really basic, but I can't figure it out.
>
> I want to start R so that I can specify the location for the Library tree. In principel simple:
>
> As I only want it dependent on the directory I stat R in, I put a .Rprofile file in the directory.
>
> My default path is:
>
>> .libPaths()
> [1] "/home/rkrug/R/i686-pc-linux-gnu-library/2.15"
> [2] "/usr/lib/R/site-library"
> [3] "/usr/lib/R/library"
>>
>
> But I want to have it
>
>> .libPaths()
> [1] "/home/rkrug/THE_DIRECTORY/library"
> [2] "/usr/lib/R/library"
>>
>
> The first part is easy:
>
> .libPaths("/home/rkrug/THE_DIRECTORY/library")
>
> but how can I remove the site library?
>
> If I set
>
> In R 15.2 under Ubuntu, started with
>
> R --vanilla
>
>> .libPaths()
> [1] "/home/rkrug/R/i686-pc-linux-gnu-library/2.15"
> [2] "/usr/lib/R/site-library"
> [3] "/usr/lib/R/library"
>> .Library.site
> [1] "/usr/lib/R/site-library" "/usr/lib/R/library"
>> .Library
> [1] "/usr/lib/R/library"
>> .Library.site <- "" .Library.site
> [1] ""
>> .libPaths()
> [1] "/home/rkrug/R/i686-pc-linux-gnu-library/2.15"
> [2] "/usr/lib/R/site-library"
> [3] "/usr/lib/R/library"
>> .libPaths("") .libPaths()
> [1] "/usr/lib/R/site-library" "/usr/lib/R/library"
>> .Library
> [1] "/usr/lib/R/library"
>> .Library.site
> [1] ""
>>
>
>
>> .libPaths("") .libPaths()
> [1] "/usr/lib/R/site-library" "/usr/lib/R/library"
>>
>
> even executing
>
>> .libPaths(.libPaths())
>
> does not change anything.
>
> Am I missing something or is there a bug in .libPaths()?

I don't think there is a bug.  As ?.libPaths says,

"Function .libPaths always uses the values of .Library and .Library.site 
in the base namespace. .Library.site can be set by the site in 
‘Rprofile.site’, which should be followed by a call to 
.libPaths(.libPaths()) to make use of the updated value."

So you can't change the value of .Library.site after starting R.  You'll 
need to use environment variables (as described on that page) to do it.

Duncan Murdoch

>
> Cheers,
>
> Rainer
>
>
>
> - --
> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys.
> (Germany)
>
> Centre of Excellence for Invasion Biology
> Stellenbosch University
> South Africa
>
> Tel :       +33 - (0)9 53 10 27 44
> Cell:       +33 - (0)6 85 62 59 98
> Fax :       +33 - (0)9 58 10 27 44
>
> Fax (D):    +49 - (0)3 21 21 25 22 44
>
> email:      Rainer at krugs.de
>
> Skype:      RMkrug
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