install.packages R on Ubuntu 12.04 downloads but does not install packages

Question

I'm perplexed. I've done this process a dozen times and never had this issue.

I installed the latest version of R for Ubuntu

I enter R, no issues at all, gives me the latest version, and I can load native packages.

But When I try to install new packages, they download, but I get nothing. For example, if I install ggplot2:

> install.packages("ggplot2")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
also installing the dependencies ‘colorspace’, ‘stringr’, ‘RColorBrewer’, ‘dichromat’, ‘munsell’, ‘labeling’, ‘plyr’, ‘digest’, ‘gtable’, ‘reshape2’, ‘scales’, ‘proto’

trying URL 'http://rweb.quant.ku.edu/cran/src/contrib/colorspace_1.2-4.tar.gz'
Content type 'application/x-gzip' length 242791 bytes (237 Kb)
opened URL
==================================================
downloaded 237 Kb

trying URL 'http://rweb.quant.ku.edu/cran/src/contrib/stringr_0.6.2.tar.gz'
Content type 'application/x-gzip' length 20636 bytes (20 Kb)
opened URL
==================================================
downloaded 20 Kb

[snip ... ]

trying URL 'http://rweb.quant.ku.edu/cran/src/contrib/ggplot2_0.9.3.1.tar.gz'
Content type 'application/x-gzip' length 2330942 bytes (2.2 Mb)
opened URL
==================================================
downloaded 2.2 Mb


The downloaded source packages are in
        ‘/tmp/RtmpoPUAFL/downloaded_packages’
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’

I've completely purged files a number of times, but not with any luck.

I'm logged in as root.

I feel like I'm missing something obvious? I don't know -- I've done this same thing a dozen times on Ubuntu, Mac, Windows, and Debian. Help?

Coastguardsman

Are you on an Amazon EC2 or something similar? – Mendoza

Yes, I'm on a VPS (Digital Ocean). I've done the same install process on Linode a dozen times. Here's another clue. I just installed on a separate VPS, which will be my production server, and had no issues. – Coastguardsman

I had a similar problem when I was running a micro instance on Amazon EC2. The ram was insufficient and installing packages resulted in what you described. I fixed it by enabling some swap see #17174472 – Mendoza

also when you start R, starts as $ sudo R provided your user has sudo permissions. This allows writing into the R directory in the home directory of the default user - otherwise you may get a permission denied ! – Broadway

Answer 1

@jdharrison helped out. The problem was insufficient memory on the VPS I was running, so I added some swap as described here:

How do you add swap to an EC2 instance?

Coastguardsman

Answer 2

Look at the last lines:

The downloaded source packages are in
    ‘/tmp/RtmpoPUAFL/downloaded_packages’

You have to go to the directory /tmp/RtmpoPUAFL/downloaded_packages (cd ...) and then install them manualy in the order that is pointed out above. So

R CMD INSTALL colorspace_1.2-4.tar.gz
R CMD INSTALL stringr_0.6.2.tar.gz
R CMD INSTALL ggplot2_0.9.3.1.tar.gz

Then trylibrary(ggplot2) now it should work

I have no idea why you have to do this sometimes... I anyone knows i am happy to learn it as well.

Curio

Answer 3

If your server does not have enough ram, R can not install packages.

The solution is to either increase the physical ram, or increase the size of the swap file.

Create a 2 gig swap file

sudo fallocate -l 2G /swap.img
sudo mkswap /swap.img
sudo swapon /swap.img

You can see how much free swap is available with the swapon command

root@foo:# swapon -s
Filename                Type        Size    Used    Priority
/swap.img                               file        2097148 213388  -1

Doorsill