cboettig/treeBASE — Issue #5: installing the dependency packages RCurl and XML (is non-simple)
Author: rossmounce
Created: 2011-12-07 02:11:13+00:00
State: open

Hi guys, just thought I'd let you know I've just installed treebase and I think it's brilliant!
I hope to do some interesting phylo meta-analyses using it.
As well as checking the reproducibility of phylo research
* _evil laugh_ *

But the serious point of this post...
I just thought I'd give some feedback on my experience just getting it installed in R - it wasn't as easy as I'd hoped, even for an experienced R user. That said, it wasn't impossible either, just awkward.

It wasn't the fault of RtreeBASE, rather it's dependencies - it took a fair bit of googling around the problems to get the RCurl and XML packages installed.

[this was all on a 64-bit Ubuntu 11.10 machine]

usually, I install packages *in* R (interactively) using install.packages()

so when I did this, I quickly found that neither XML nor RCurl dependency packages (and thus RtreeBASE) would install nicely via this route. I managed to install the xml package, in a normal (non-R) terminal using:

sudo apt-get install r-cran-xml

then thanks to this beautifully concise post here:
http://haotu.wordpress.com/2011/05/26/install-bioconductor-rcurl-ubuntu/

I installed an ubuntu package with:

sudo apt-get install libcurl4-gnutls-dev

and then proceeded to successfully install the RCurl and RtreeBASE packages

*phew*
I hope this helps others install / use RtreeBASE.