Hi ,

Your advices is quite great!
i don't know how to create .Rprofile until see your advices
Thanks


On 10/25/06, James W. MacDonald <jmacdon@med.umich.edu> wrote:
>
> 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.
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
> --
> 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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>



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