R Install Dependencies

Consider the following situation. You need to install a set of R packages on a machine that cannot make external http(s) requests. As such, you must download source files for the pacakge, along with all of the dependencies, and dependencies of dependencies, etc, and transfer these source files to the machine (likely via FTP) that cannot make the external http(s) requests. Further, you need to install the packages in the correct order so that the install of a dependency does not fail do to a missing dependencies of the the dependency.

The scrpt build-dep-list.R will generate the needed list of dependencies, download the source files, from both CRAN and BioConductor, and then generate a Makefile to install the packages in an order so that R package dependencies should not cause errors.

Use

On a computer, with internet access run the following script

Rscript --vanilla build-dep-list.R pkg1 [pkg2] [pkg3] [...] [pkgn]

The R script will download the source (.tar.gz) file for pkg1 and the dependencies (packages listed under Depends, Imports, and LinksTo in the DESCRIPTION file) along with the dependencies of the dependencies, and so on. You may list multiple packages here and the n packages and dependencies will be downloaded.

Alternatively, you could list the wanted packages in a file, say getthese.txt, and call this function thusly:

Rscript --vanilla build-dep-list.R getthese.txt

The source files for each package and all dependencies will be placed in a pkg-source-files directory.

The R script will generate a Makefile

After transfering the Makefile and the pkg-source-files directory to the remote machine, the user need only to run GNU make the needed packages.

make

Example

Say you need to download three packages: 1. ggplot2, 2. qwraps2, 3. data.table.

Rscript --vanilla build-dep-list.R ggplot2 qwraps2 data.table

or

echo -e "ggplot2\nqwraps2\ndata.table" > needed-pkgs.txt
Rscript --vanilla build-dep-list.R needed-pkgs.txt

Pausing between file downloads

If you want/need to have a notable pause between downloads of each package then you can add an optional command line argument --pause=N and a minimum of N seconds will lapse between downloads.

Rscript --vanilla build-dep-list.R --pause=3 qwraps2 cpr data.table