On 30/08/2010 6:00 PM, Atkinson, Elizabeth J. (Beth) wrote:
Several of us locally are puzzling over the following problem:
We have a central repository of R packages on our linux system.
Occasionally, we'd like to install a different version of the same
package (such as making updates to the survival package before it is
released to the larger group, or a downloaded beta version). When
using the library function, it appears that lib.loc is not being used
and instead the central repository is being used. We've even tried
modifying .libPaths( ) so that our local path is first in the search
list. Is this a bug or a "feature"?
For example:
>
install.packages('DBI',lib='/data1/bsi/epi/s105816.SNPlinkage/CNV/rlib')
> library(DBI,
lib.loc='/data1/bsi/epi/s105816.SNPlinkage/CNV/rlib')
I can look in my directory and see that DBI is version 0.2-5,
but when I use the library command I get the version installed in the
central location instead of in my specified directory.
> library(help=DBI)
You didn't specify the lib.loc in this command. Typing library() will
tell you where it will look, in the order given by .libPaths().
Duncan Murdoch
Information on package 'DBI'
Package: DBI
Version: 0.2-4
Title: R Database Interface
Author: R Special Interest Group on Databases (R-SIG-DB)
Maintainer: David A. James <daj...@gmail.com>
Depends: R (>= 2.3.0), methods
LazyLoad: yes
License: LGPL (version 2 or later)
Collate: DBI.R Util.R zzz.R
Packaged: Tue Oct 16 21:43:31 2007; dj
Built: R 2.10.0; ; 2009-10-26 17:51:14 UTC; unix
Further information is available in the following vignettes in
directory
'/usr/local/biotools/r/R-2.10.0/lib64/R/library/DBI/doc':
version
_
platform x86_64-unknown-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 2
minor 10.0
year 2009
month 10
day 26
svn rev 50208
language R
version.string R version 2.10.0 (2009-10-26)
Beth Atkinson, MS | Statistician III | Division of Biomedical Statistics
& Informatics| Assistant Professor of Biostatistics
Phone: 507-284-0431 | Admin Assistant: 507-266-4556 | Fax: 507-284-9542
| atkin...@mayo.edu
Mayo Clinic | 200 First Street SW | Rochester, MN 55905 |
www.mayoclinic.org
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and provide commented, minimal, self-contained, reproducible code.
