[BioC] Installing bioconductor under MacOsx

[Robert Gentleman]

Well, not wanting to be too contradictory, it would be better if we
didn't presume that we could write all over the users machine...that
will get fixed. The package managment tools need to function in
environments where not all R libraries are writable by the user; an
oversight on our part which we will rectify.

Thanks for the bug report.

  Robert

On Thu, May 01, 2003 at 12:35:14PM -0400, Warnes, Gregory R wrote:
> 
> 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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> > sketchy/use Email 
> > UW  : Th: 206-543-1044 (fax=3286)|Change last 4 digits of 
> > phone to FAX 
> > 
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-- 
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| Robert Gentleman                 phone : (617) 632-5250                   |
| Associate Professor              fax:   (617)  632-2444                   |
| Department of Biostatistics      office: M1B20                            |
| Harvard School of Public Health  email: rgentlem at jimmy.harvard.edu        |
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