Question: biocLite installing to tmp directory
1
gravatar for Naomi Altman
5.6 years ago by
Naomi Altman6.0k
Naomi Altman6.0k 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" Naomi
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ADD COMMENTlink modified 5.6 years ago by James W. MacDonald51k • written 5.6 years ago by Naomi Altman6.0k
Answer: biocLite installing to tmp directory
0
gravatar for James W. MacDonald
5.6 years ago by
United States
James W. MacDonald51k 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
ADD COMMENTlink written 5.6 years ago by James W. MacDonald51k
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 >> >> _______________________________________________ >> 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
ADD REPLYlink written 5.6 years ago by Naomi Altman6.0k
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 >
ADD REPLYlink written 5.6 years ago by Dan Tenenbaum8.2k
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