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Question: Installation of bioConductor packages
0
2.9 years ago by
av0
Norway
av0 wrote:

Dear Bioconductor users, how can I install complete list of BioConductor packages?
For example all packages from this list:
https://www.bioconductor.org/packages/release/BiocViews.html#___Software

Sincerely yours,
Andrey

modified 2.9 years ago by Martin Morgan ♦♦ 22k • written 2.9 years ago by av0
2
2.9 years ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

Are you sure you want to do this? There are a lot of packages, and it's unlikely that your users will want all of them.

Naively, you could get a vector of all packages and install them and their dependencies. For some, you will likely need to install both simple (e.g., libcurl-dev, libxml2-dev) and complex system dependencies. At the end of the day you will be able to say

source("https://bioconductor.org/biocLite.R")
pkgs = available.packages(repos=biocinstallRepos())
biocLite(rownames(pkgs))

A better strategy is likely to create a local mirror of the Bioconductor CRAN-style repository, and then to install / update from there. See the siteRepos argument to BiocInstaller::biocLite(), and the repos argument to install.packages(). (Use biocLite() rather than install.packages() for installation, to more correctly manage R / Bioconductor versions).

Probably though you have several users that you are trying to support. Then the strategy is to allow users to install packages into their personal libraries, which is how R works 'out of the box' -- install R system wide; when a user tries to install a package via instructions on any package landing page (e.g., IRanges) they'll be prompted to create their own library in a characteristic location. You could have a core of packages installed centrally, e.g., by running under the account used to install R the commands

source("https://bioconductor.org/biocLite.R")
biocLite()

and perhaps other packages that you find are used by several users. But in the end I think this kind of 'management' is a dis-service, at least to 'regular' users (maybe it is a benefit to novice users; 'advanced' users will just avoid the system installation). Perhaps there are security policy constraints at your location that don't allow this sort of user independence; investigate changing those policies. There is some guidance in section 6 of the R-admin manual.