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On 15/02/13 15:41, Duncan Murdoch wrote:
> On 13-02-15 9:28 AM, Rainer M Krug wrote: 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.
Thanks for the clarification - the use of the word "site" in "set by the site
in ‘Rprofile.site’ "
was not clear to me. I thik it would be much clearer, if it states that the
variables .Library and
.Library.site can not be changed while R is running although it looks as if
they can be changed
(but then new ones in the top environment are created).
Now just one more question: where can I see that
.Library <- "/A/New/Existing/Directory"
has no impact?
I expected to see this in the code of .libPaths, but I didn't:
> .libPaths
function (new)
{
if (!missing(new)) {
new <- Sys.glob(path.expand(new))
paths <- unique(normalizePath(c(new, .Library.site, .Library),
"/"))
.lib.loc <<- paths[file.info(paths)$isdir %in% TRUE]
}
else .lib.loc
}
<bytecode: 0x88e7640>
<environment: 0x88e685c>
>
Thanks,
Rainer
>
>> Duncan Murdoch
>
>
> Cheers,
>
> Rainer
>
>
>
>>
>> ______________________________________________ R-help@r-project.org mailing
>> list
>> https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html and provide commented, minimal,
>> self-contained,
>> reproducible code.
>>
>
- --
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: rai...@krugs.de
Skype: RMkrug
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