Manually Downloading and Installing Packages in R

Question

I am currently trying to run some R code on a computing cluster but cannot run the install.packages function due to some weird firewall settings on my cluster. Since I am only using a few packages in my R code, I was hoping to avoid using the install.packages function by downloading and installing the packages manually.

Note: I am aware that there is a way to avoid this issue by using an HTTP proxy as described in the R FAQ. Unfortunately the people in charge of my cluster are not being helpful in setting this up so I'm forced to consider this alternative approach.

Ideally, I would like to download the packages files from CRAN to my computer, then upload these files to the cluster and install them using the appropriate commands in R. In addition, I would also like to make sure that the packages are installed to a location of my choice since I do not have the permission to "write" in the default R directory (I believe that I can do this within R by using the .libPaths function)

Lastly, the computers that I am working with on the cluster are Unix x86_64.

Doubleminded

It's certainly possible to do this, and the install.packages function will accept a NULL repository argument. – Mcevoy

Awesome! I didn't realize this at all. Just to confirm the following snippet should work, correct? install.packages(pkgs = MyListofTARGZFiles, repos = NULL, lib = MyLibraryDirectory) – Doubleminded

Not sure exactly that formalism would work, assuming it is really a list. The first argument needs to be a character vector. – Mcevoy

I wonder where do you get the .tar.gz source packages in the first place? – Ownership

Found it: cran.r-project.org/web/packages/available_packages_by_name.html – Ownership

Answer 1

You can install the package manually using the following command

install.packages('package.zip', lib='destination_directory',repos = NULL)

See the help of ?install.packages, for further description

Indebtedness

Thanks! Just to make sure: since I'm working on UNIX computers, shouldn't the packages be in tar.gz format? – Doubleminded

If you have the package source .tar.gz it should work as well – Indebtedness

In my case, this throws an error telling a NAMESPACE file is required. > install.packages('/Users/arun/Desktop/DiagnosisMed_0.2.3.tar.gz', lib="~/Library/R/3.3/library/", repos = NULL) * installing *source* package ‘DiagnosisMed’ ... ERROR: a 'NAMESPACE' file is required * removing ‘/Users/arun/Library/R/3.3/library/DiagnosisMed’ Warning in install.packages : installation of package ‘/Users/arun/Desktop/DiagnosisMed_0.2.3.tar.gz’ had non-zero exit status – Alvinalvina

how do you download packages as zip files ? – Perigee

Answer 2

I also went through the same problem while installing the caret package. There are many dependencies of the caret package. So, I did the following:

install.packages('caret'): This gives all packages in zip format the location of download is shown in the error message. Unzip all packages from download source to a location for example in C:/PublicData/RawRPackages, then run following command.

foldername <- 'C:/PublicData/RawRPackages'
install.packages(paste(foldername, 'caret', sep = '/'),
                 repos = NULL, type = "source")
library(caret, lib.loc = foldername)

Pyrrhuloxia

Your solution is very useful, because it is not necessary to know the destination directory of the package! It is found automatically. – Bergwall

Answer 3

this the better way, if we want to download and install locally :

download.packages('lib_name',destdir='dest_path')

for example :

download.packages('RJDBC',destdir='d:/rlibs')

Hoskinson

Am I missing something, or does this not pull down dependencies? – Thayer

Answer 4

install.packages("libname",lib = "file://F:/test")

Briticism

I added it because myself had problems with the format of library. Thought maybe it helps someone else! – Briticism