[BioC] biocLite installing to tmp directory

[James W. MacDonald]

Hi Naomi,

On Wednesday, April 09, 2014 12:07:11 PM, NAOMI S ALTMAN wrote:
> biocLite is installing to a tmp directory instead of my (writeable) R
> library directory.  I can fix this using "destdir" but when I am
> prompted for updates to other libraries, these are still being
> installed in tmp.
>
> This behavior appears to have started when I started using RStudio,
> but perhaps this is a co-incidence.
>
> "The downloaded binary packages are in
> C:\Users\nsa1\AppData\Local\Temp\Rtmp46NiD9\downloaded_packages"

This doesn't indicate where the package is being installed, but where 
it is being downloaded prior to being installed. And destdir only 
controls where the packages get downloaded to, not where they get 
installed.

The installation location is directed by the output from .libPaths(), 
unless you specify a particular lib location in the call to biocLite 
(and the default for biocLite is to use .libPaths()), so if you have a 
reasonable output from .libPaths(), and are not specifying a lib 
argument to biocLite, the packages are being installed in the correct 
place.

Best,

Jim


>
> Naomi
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099