On 3 July 2017 at 13:05, Ramon Diaz-Uriarte wrote: | If I might chime in, I'd like to add my vote to the "users should be able | to use install.packages and should be able to install bioconductor | packages with biocLite". | | Longer story | ============ | | Two cases (I've just faced this morning), where | /usr/local/lib/R/site-library/ was not user-writeable: | | 1. Students using Debian or Ubuntu on their laptops, where these students | are not particularly knowledgeable about Linux. | | 2. Sys admins that install and configure software for computer labs, where | beyond some bare minima (e.g., R, gcc, etc) users are expected and allowed | to install (some) software on their homes. These sys admins might be | specially reluctant to add users to privileged groups and/or make | /usr/local/lib/R/site-library user-writeable. | | The problem is that both groups, after issuing the | | sudo apt-get install r-base | sudo apt-get install r-base-dev | | (as per https://cran.r-project.org/bin/linux/ubuntu/README.html) | | are later surprised when users cannot immediately install packages in the | "usual R way (install.packages)". And this gets more complicated when we | add a bunch of bioconductor packages, where BioConductor pages often say to | install as | | source("https://bioconductor.org/biocLite.R";) | biocLite(some_packages) | | I've ended up doing | | .libPaths(c(the_user_home, .libPaths())) | | but this does not look very friendly for new users.
Easier: Remove one # comment character in /etc/R/Renviron which does the same. As does setting in file /etc/R/Renviron.site (which the package never touches). And local policy can (and should!) still be to set a local group. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org _______________________________________________ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
