R help - May 2010 - library location and error messages when loading packages

Hello,

I am running R on a server that several people share. Previously we
all had separate libraries for R.
I have set up R so everyone on the server shares the same library and
I downloaded the latest version of R and installed it on the
main drive of our server in the  "Program Files" folder (obvious
enough).

I changed the Environmental Variables in the advanced system setting
so R_LIBS  is C:\\RLIBRARY and restarted the server.

The commands :
>.libPaths()
[1] "C:\\RLIBRARY"                   
"C:/PROGRA~1/R/R-211~1.0/library"
> .Library
[1] "C:/PROGRA~1/R/R-211~1.0/library"


 When I try to run several packages it says It can not load them
(although many packages do work). So I tried
to install the  packages again (I deleted the old ones, downloaded a zip file
of the new ones  and this is what happened :
> library(Hmisc)
Error in library.dynam(lib, package, package.lib) :
 shared library 'cluster' not found
Error: package/namespace load failed for 'Hmisc'

utils:::menuInstallPkgs()
trying URL
'http://cran.ms.unimelb.edu.au/bin/windows/contrib/2.11/cluster_1.12.3.zip'
Content type 'application/zip' length 340188 bytes (332 Kb)
opened URL
downloaded 332 Kb
package 'cluster' successfully unpacked and MD5 sums checked
The downloaded packages are in
       C:\Users\Daisy
Englert\AppData\Local\Temp\2\RtmpWGZV31\downloaded_packages

>library(cluster)
Error in get(Info[i, 1], envir = env) :
 internal error -3 in R_decompress1
Error: package/namespace load failed for 'cluster'


******But, I can fix this by setting the lib.loc
> library(cluster, lib.loc =  "C:/PROGRA~1/R/R-211~1.0/library" )
******Unfortunately this is not where the updated packages went, the
updated package went to  "C:\\RLIBRARY" . I have messed something up
and I do not know how to fix it.

Any advice would be welcome.


Thanks,
Daisy

-- 
Daisy Englert Duursma

Room E8C156
Dept. Biological Sciences
Macquarie University  NSW  2109
Australia

On 24.05.2010 03:59, Daisy Englert Duursma wrote:
> Hello,
>
> I am running R on a server that several people share. Previously we
> all had separate libraries for R.
> I have set up R so everyone on the server shares the same library and
> I downloaded the latest version of R and installed it on the
> main drive of our server in the  "Program Files" folder (obvious
> enough).
>
> I changed the Environmental Variables in the advanced system setting
> so R_LIBS  is C:\\RLIBRARY and restarted the server.
>
> The commands :
>> .libPaths()
> [1] "C:\\RLIBRARY"                   
"C:/PROGRA~1/R/R-211~1.0/library"

1. So this is a Terminal Server, not a network drive, right?

>> .Library
> [1] "C:/PROGRA~1/R/R-211~1.0/library"
>
>
>   When I try to run several packages it says It can not load them
> (although many packages do work). So I tried
> to install the  packages again (I deleted the old ones, downloaded a zip
file
> of the new ones  and this is what happened :
>
>> library(Hmisc)
> Error in library.dynam(lib, package, package.lib) :
>   shared library 'cluster' not found
> Error: package/namespace load failed for 'Hmisc'

Strange, since cluster is a recommended package. Have you inspected the 
permissions in the directory of your R installation?


> utils:::menuInstallPkgs()
> trying URL
'http://cran.ms.unimelb.edu.au/bin/windows/contrib/2.11/cluster_1.12.3.zip'
> Content type 'application/zip' length 340188 bytes (332 Kb)
> opened URL
> downloaded 332 Kb
> package 'cluster' successfully unpacked and MD5 sums checked
> The downloaded packages are in
>         C:\Users\Daisy
> Englert\AppData\Local\Temp\2\RtmpWGZV31\downloaded_packages
>
>
>> library(cluster)
> Error in get(Info[i, 1], envir = env) :
>   internal error -3 in R_decompress1
> Error: package/namespace load failed for 'cluster'
>
>
> ******But, I can fix this by setting the lib.loc
>
>> library(cluster, lib.loc =  "C:/PROGRA~1/R/R-211~1.0/library"
)
>
> ******Unfortunately this is not where the updated packages went, the
> updated package went to  "C:\\RLIBRARY" . I have messed something
up
> and I do not know how to fix it.
At first, look at write / read permissions in both libraries.

Uwe Ligges

>
> Any advice would be welcome.
>
>
> Thanks,
> Daisy
>