[BioC] A question about installation of cghFLasso package

[affy snp]

Hi Sean,

Thanks a lot!

I tried biocLite() earlier and then switched to R CMD INSTALL.

I just did it once again and got:

(1) For server 1,

> source('http://bioconductor.org/biocLite.R')
> biocLite('cghFLasso')
Running biocinstall version 2.1.8 with R version 2.6.0
Your version of R requires version 2.1 of Bioconductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  argument 'lib' is missing: using
'/home/allen/R/x86_64-redhat-linux-gnu-library/2.6'
trying URL 'http://cran.fhcrc.org/src/contrib/cghFLasso_0.1-2.tar.gz'
Content type 'application/x-gzip' length 142390 bytes (139 Kb)
opened URL
==================================================
downloaded 139 Kb

ERROR: failed to lock directory
'/mnt/sc03/genomics/home/allen/R/x86_64-redhat-linux-gnu-library/2.6'
for modifying
Try removing '/mnt/sc03/genomics/home/allen/R/x86_64-redhat-linux-gnu-library/2.6/00LOCK'

The downloaded packages are in
        /tmp/Rtmp2UkIQF/downloaded_packages
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  :
  installation of package 'cghFLasso' had non-zero exit status
>

(2) For server 2,

> source('http://bioconductor.org/biocLite.R')
> biocLite('cghFLasso')
Running biocinstall version 2.0.8 with R version 2.5.0
Your version of R requires version 2.0 of Bioconductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
         argument 'lib' is missing: using '/home/allen/lib/R'
trying URL 'http://cran.fhcrc.org/src/contrib/cghFLasso_0.1-2.tar.gz'
Content type 'application/x-gzip' length 142390 bytes
opened URL
==================================================
downloaded 139Kb

* 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'

The downloaded packages are in
        /tmp/RtmpbuM77p/downloaded_packages
Warning messages:
1: installation of package 'cghFLasso' had non-zero exit status in:
install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,
2: cannot create HTML package index in: tools:::unix.packages.html(.Library)
>



Thanks a lot!

Allen




On Nov 10, 2007 4:13 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> 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
>