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 > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor at r-project.org > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -- > > James W. MacDonald, M.S. > > Biostatistician > > University of Washington > > Environmental and Occupational Health Sciences > > 4225 Roosevelt Way NE, # 100 > > Seattle WA 98105-6099 > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >