GenomicFeatures Package Installation Trouble

Question

Sorry to be back so soon with a simple installation question, but my inability to solve it myself is seriously impairing my productivity. Anyway, I tried installing GenomicFeatures as suggested by the BC website.

> source("http://bioconductor.org/biocLite.R")
> biocLite("GenomicFeatures")

I received the following error messages (in addition to several warning messages)

ERROR: configuration failed for package ‘RCurl’
* removing ‘/home/tim/R/i686-pc-linux-gnu-library/2.15/RCurl’
ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘rtracklayer’
* removing ‘/home/tim/R/i686-pc-linux-gnu-library/2.15/rtracklayer’
ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘biomaRt’
* removing ‘/home/tim/R/i686-pc-linux-gnu-library/2.15/biomaRt’
ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘RCurl’ are not available for package ‘GenomicFeatures’
* removing ‘/home/tim/R/i686-pc-linux-gnu-library/2.15/GenomicFeatures’

So some problem with the dependencies I guess, but it seems strange that they would be automatically installed prior to GF. I am using version 2.15.0. Any clue as to what the problem might be? I'd be happy to provide more info as needed. Thanks.

Answer 1

Martin Morgan has a solution that I believe works in the comments. I'll elaborate on that a little bit.

The error messages are telling you that you need the RCurl and XML packages installed. Both of these packages require that your system has certain development packages on them. You appear to be running Linux. If you're using a Debian based system (Debian, Ubuntu, Mint, ...) then for RCurl to install you need to install libcurl4-openssl-dev and for XML to install you need to install libxml2-dev. You can accomplish this by relatively easily on the command line by typing

sudo apt-get install libcurl4-openssl-dev libxml2-dev

That should install the required packages and any dependencies. Then you should be able to install the RCurl and XML packages from within R.

install.packages("RCurl")
install.packages("XML")

At this point you have the required dependencies and should be able to install GenomicFeatures from Bioconductor.

source("http://bioconductor.org/biocLite.R")
biocLite("GenomicFeatures")

Just a note for those using Windows - getting RCurl and XML isn't necessarily easy, however, Dr. Brian Ripley provides binaries for these packages at his website and you can download them from there quite easily. Initially when I saw there was issues with RCurl and XML I thought it must be a windows user until I looked at the actual errors and realized it was a Linux user.