[BioC] Installing bioconductor under MacOsx

[A.J. Rossini]

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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