[BioC] R-package installation from source code

[James MacDonald]

If you look at the code for getBioC, you will see that there is a
variable you can pass called 'destdir'. If you simply change your
function call to:

getBioC("release",destdir="home/rlv10/r181/library")

this should use the correct library path.

HTH,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
>>> "Roger Vallejo" <rvallejo at psu.edu> 12/23/03 3:31 PM >>>
I installed the R-package from source code in a linux readhat 7.3. The
program runs. The problem is when I tried to install (or update) new
packages and libraries. The new install and libraries goes by default to
folders that I have no access (I am not the unix/linux administrator)
such as /usr/global/R-1.8.0/lib/R/library.   After this problem, I
re-installed the R-package making sure that the installation should go
to my home directory (home/rlv10/r181/library). But after installing and
running R, still the updates/installation of packages/libraries is send
to the undesired folder (/usr/global/R-1.8.0/lib/R/library). Why is
that?

I asked my local unix/linux admistrators, they are still working on that
and meanwhile I thought someone from the R group may know how to fix
this problem.

 

This is the error message:

************************************************************************
*********

> source("http://www.bioconductor.org/getBioC.R")

> getBioC(relLevel="release")

Running getBioC version 1.2.46....

If you encounter problems, first make sure that

you are running the latest version of getBioC()

which can be found at: www.bioconductor.org/getBioC.R

 

Please direct any concerns or questions to
bioconductor at stat.math.ethz.ch.

 

Error in getBioC(relLevel = "release") : You do not have write access to
/usr/global/R-1.8.0/lib/R/library 

Please check your permissions or provide a different 'destdir' parameter

>

***************************************************************

 

Perhaps a quick fix could be to add a different "destdir" in the
command:

 

> getBioC(relLevel="release")

 

How to do that?

Thanks in advance for the hand!

 

Roger

 

 

 

 


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