[BioC] Assistance: mouse4302cdf installation

[James W. MacDonald]

Hi Melissa,

It appears your sysadmin is pretty responsive (you do have the newest 
release of R installed after all), so you may be able to take Li and 
Kasper's advice.

However, there is a simple option you can take that will allow you to 
install an arbitrary number of packages without having to bother the 
sysadmin every time you want to add another. Just create a directory 
somewhere that you do have privileges (e.g., /home/<Melissa's 
home>/R_library) and then use .libPaths() to set this as a library. You 
will also need to create a .Rprofile file in your home directory as 
well, so every time you start R it will know about the library.

The .Rprofile file will only need to contain one line:

.libPaths("/home/<Melissa's home>/R_library")

You could also add

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

so you can use biocLite() to install things without having to explicitly 
source the function every time. I have this in my .Rprofile because I 
get really tired of typing the above line every time I want to install 
something.

Best,

Jim

Melissa Paczkowski wrote:
> We are using the newest version of Bioconductor (1.9) to perform an Affy 
> microarray analysis on some mouse chips.  When we start using the "expresso" 
> command to normalize the signal intensity, we get the following error statement:
>  
> "mkdir: "/usr/local/R-2.4.0/lib/R/library/00LOCK": Permission denied
> ERROR: failed to lock directory '/usr/local/R-2.4.0/lib/R/library' for modifying
>  
> The downloaded packages are in
>         /tmp/Rtmpi41v2y/downloaded_packages
> Error in getCdfInfo(object) : Could not obtain CDF environment, problems 
> encountered:
> Specified environment does not contain Mouse430_2
> Library - package mouse4302cdf not installed
> Data for package affy did not contain mouse4302cdf
> Library - package mouse4302cdf not installed
> In addition: Warning messages:
> 1: installation of package 'mouse4302cdf' had non-zero exit status in: 
> install.packages(cdfname, lib = lib, repos = Biobase:::biocReposList(),  
> 2: cannot create HTML package index in: tools:::unix.packages.html(.Library)" 
> 
> We downloaded "mouse4302cdf_1.12.0.tar.gz", but we cannot install it.  We tried 
> to use the following R commands to install this package:
>  
> install.packages("mouse4302cdf")
> install.packages2("mouse4302cdf")
> attach(mouse4302cdf)
> biocLite("mouse4302cdf")
>  
> We also tried installing the "getBioC" package from the 
> www.bioconductor.org/download   .
>  
> Thank you for your help.
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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