[BioC] Installing bioconductor under MacOsx

[Byron Ellis]

As others have said, you don't have write access.... Set your R_LIBS in 
your .tcshrc (or .bash_profile if you're a bash user). I like
setenv R_LIBS /Users/<username>/Library/R

using bash:
export R_LIBS=/Users/<username>/Library/R

This puts user installed packages (including Bioconductor---it works 
fine on my iBook) in ~/Library/R rather than trying to use the system 
repository. If you want to make the packages available to all users you 
might want to consider using /Users/Shared/R or something like that 
instead.

You should make sure to mkdir ~/Library/R before you try it though :-)

You can also create a file ~/.MacOSX/environment.plist which is a 
standard plist (search macosxhints.com for the format if you like... or 
use the PList editor that comes with the Developer Tools) that makes 
the environment variables available to _ALL_ OS X applications (after 
logging in and out of course). This is useful if, say, you were going 
to use StatPaper and wanted to have a custom R package location.

Hope that Helps,
	B



On Thursday, May 1, 2003, at 11:33  AM, Martino Barenco wrote:

> 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
>
> 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?
>
> Other Information:
>
> -The version of R I use is 1.7.0 and was installed via fink:
>
> > R.version
>          _
> platform powerpc-apple-darwin6.5
> arch     powerpc
> os       darwin6.5
> system   powerpc, darwin6.5
> status
> major    1
> minor    7.0
> year     2003
> month    04
> day      16
> language R
>
> I also tried the whole thing via the carbon version of R (1.6.2), 
> which works fine, except that it has no widgets and the 
> functionalities I am interested in (normalisation/summary procedures 
> in the "affy" package) crash because of some Fortran/C thing missing.
>
> Thanks a lot
>
> Best regards
>
> Martino
>
> ---------------------------------------
> Martino Barenco
> CoMPLEX
> 4, Stephenson Way
> London NW1 2HE
> Tel.: +44 20 7679 5088
> Fax.: +44 20 7383 5519
> Email: 
> m.barenco at ucl.ac.uk_______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
Byron Ellis (bellis at hsph.harvard.edu)
"Oook" - The Librarian
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