[BioC] Installing bioconductor under MacOsx

[Warnes, Gregory R]

It is probably a better idea to change the ownership of the library
directory, so that you need not be root in order to install.

Something like

	sudo chown username /sw/lib/R/library

then do the install.  

-Greg
	

> -----Original Message-----
> From: rossini at blindglobe.net [mailto:rossini at blindglobe.net]
> Sent: Thursday, May 01, 2003 12:28 PM
> To: Martino Barenco
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Installing bioconductor under MacOsx
> 
> 
> Martino Barenco <sejjmba at ucl.ac.uk> writes:
> 
> 
> > Hi,
> >
> > I am running R under X11 (MacOsx) and when I try to install
> > bioconductor (Unix/Linux procedure), I get the following message:
> >
> >> getBioC(libName="all")
> > Running getBioC version 1.2.28....
> > 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(libName = "all") : You do not have write access to
> > /sw/lib/R/library
> > Please check your permissions or provide a different 'destdir'
> > parameter
> 
> Sounds like you need to install as root, in this case, i.e. sudo R and
> then go on.   BUT, you probably REALLY do not want to do this.  I
> mean, REALLY do not want to do this (should I say it a 3rd time?).
> 
> 
> > Then, trying the "destdir" option, I get:
> >
> >>
> > 
> getBioC(libName="all",destdir="/Users/martinobarenco/Desktop/biocond")
> > Running getBioC version 1.2.28....
> > 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.
> >
> > [1] "Installing reposTools ..."
> > ERROR: cannot write to or create directory '/sw/lib/R/library'
> > Error in upDatePkgs(relLevel, PLATFORM, destdir, method = method) :
> >         Failed to install package Biobase
> >
> > What should I do?
> 
> Looks like a bug in the installer function.  Jeff?
> 
> best,
> -tony
> 
> -- 
> A.J. Rossini rossini at u.washington.edu 
> http://software.biostat.washington.edu/ 
> Biostatistics, U Washington and Fred Hutchinson Cancer Research Center
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