The warning is appropriate. Wolfgang and I are disagreeing with Steve's suggestion that the OP should just update/install as administrator. Best, Kasper On Mon, Jun 2, 2014 at 3:15 PM, Martin Morgan wrote: > On 06/02/2014 07:28 AM, Kasper Daniel Hansen wrote: > >> And as a followup: what I do in a multi-user environment (and after some >> years of experience I think this is the best approach) is to immediately >> make a site-library directory where I install all packages. Basically we >> have groups like >> 1) me >> 2) people allowed to install R packages system-wide >> 3) most users >> I set the permissions of site-library to be 2), but the standard library >> is >> always 1) because it is installed as part of R. This mean any user in 2) >> who (say) tried to update all installed R packages system-wide will be >> told >> that the packages included with R cannot be updated; exactly the situation >> the OP described. >> > > I went looking in the R-admin manual for best practices along these lines, > and was a little surprised not to see anything. Did I miss something? > > The warning seems worth-while, even if the person receiving the message is > not in a position to do anything about it; maybe they'll hassle their sys > admin? Is there a better way of phrasing the message to make it more > informative / tolerable? > > Martin > >> >> Best, >> Kasper >> >> >> >> >> On Sun, Jun 1, 2014 at 8:19 AM, Wolfgang Huber wrote: >> >> >>> On 31 May 2014, at 23:53, Steve Lianoglou >>> wrote: >>> >>>> On Sat, May 31, 2014 at 1:46 PM, Felix Francis [guest] >>>> >>>>> While trying to install Bioconductor, I get this warning message: >>>>> installed directory not writable, cannot update packages 'boot', >>>>> >>>> 'class', 'cluster', 'foreign', 'KernSmooth', 'lattice', 'MASS', >>> >>>> 'Matrix', 'mgcv', 'nlme', 'nnet', 'rpart', 'spatial' >>>>> >>>> >>>> It sounds like you do not have permissions to write into the installed >>>> directory that R was installed in on the computer you are using. >>>> >>>> Running the update/install as an administrator on the machine would >>>> likely do the trick. >>>> >>> >>> Depending on how valuable the machine is, or how many users work with it, >>> it is preferable to install R as well as its libraries with an account >>> with >>> limited rights; and then to use that account also for package updates and >>> the installation of additional packages, as what Felix is trying to do. >>> >>> Doing it as administrator seems like leaving a hole for through which bad >>> things could be done (intentionally or unintentionally) . I’ve not yet >>> seen >>> >>> this actually happening, though. >>> >>> Wolfgang >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> [[alternative HTML version deleted]] >> >> >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane. >> science.biology.informatics.conductor >> >> > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > [[alternative HTML version deleted]]