[BioC] biocLite installing to tmp directory

Dan Tenenbaum dtenenba at fhcrc.org
Wed Apr 9 18:55:36 CEST 2014


Hi Naomi,

----- Original Message -----
> From: "NAOMI S ALTMAN" <naomi at stat.psu.edu>
> To: "James W. MacDonald" <jmacdon at uw.edu>
> Cc: bioconductor at r-project.org
> Sent: Wednesday, April 9, 2014 9:51:31 AM
> Subject: Re: [BioC] biocLite installing to tmp directory
> 
> Thanks for this explanation Jim.  However, subsequently when I try to
> load the libraries they appear not to be available.  (My .libPaths()
> looks fine.)
> 

If you could send the full output of your attempt to load the packages, as well as the output of .libPaths() and sessionInfo() that would be great. For that matter, a transcript of your biocLite() command would also be helpful.

Dan


> --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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> >> Bioconductor at r-project.org
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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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> > Bioconductor at r-project.org
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> 
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