[BioC] A question about installation of cghFLasso package

[Sean Davis]

On Nov 10, 2007 3:52 PM, affy snp <affysnp at gmail.com> wrote:
> Dear list,
>
> Hello! My name is Allen Shore, a graduate student at Wistar
> Institute in Philadelphia. I am trying to use cghFLasso to
> analyze a bunch of Affy SNP array data for identifying
> copy number variations.
>
> I had no problem with installing cghFLasso package on
> windows desketop. But I did have trouble with installing
> on the server (unix system).
>
> I tried two servers and got the following errors.
>
> For Server1:
>
> [shoreallen at madison download]$ R CMD INSTALL cghFLasso_0.1-2.tar.gz
> * Installing to library '/home/allen/lib/R'
> * Installing *source* package 'cghFLasso' ...
> /usr/local/lib/R/bin/INSTALL: ./configure: /bin/sh: bad interpreter:
> Permission denied
> ERROR: configuration failed for package 'cghFLasso'
> ** Removing '/home/allen/lib/R/cghFLasso'

Hi, Allen.

This looks like a permissions problem.  Typically, if R is installed
as root, the directories for packages are owned by root.

Now, a couple of suggestions:

1)  USE biocLite() whenever possible.  It will typically do the right
thing by getting the correct package for your os and R package from
the correct repository as well as dependencies.  Also, if you are not
the Root user, it will use R to ask you for a location that makes
sense to install packages into in your local directory.

2)  If possible, ask a root user to install the packages (again, using
biocLite()) as the root user so that everyone on your machine has
access.

3)  While it seems silly to do all the time, include sessionInfo for
ALL emails if there is ANY doubt about what machine, OS, R version, or
loaded packages are being used.  I have never seen anyone faulted for
including sessionInfo unnecessarily.

So, try:

source('http://bioconductor.org/biocLite.R')
biocLite('bghFLasso')

and let us know how it went if you have problems.

Sean