On 13-02-15 9:54 AM, Rainer M Krug wrote:
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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?
If you look at environment(.libPaths) you'll see that it is not
.GlobalEnv, so the .lib.loc assignment might not happen where you think.
Indeed,
ls(environment(.libPaths), all=TRUE)
will show that it contains one object, .lib.loc. You can modify that
variable, but it's quite a risky (in the sense of being undocumented and
unsupported) thing to do.
Duncan Murdoch
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
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- --
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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