[BioC] biocLite installing to tmp directory

[NAOMI S ALTMAN]

Thanks for this explanation Jim.  However, subsequently when I try to 
load the libraries they appear not to be available.  (My .libPaths() 
looks fine.)

--Naomi


On 4/9/2014 12:17 PM, James W. MacDonald wrote:
> 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
>
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