(*Note: A new version of this post following my switch from Ubunto to OpenSuse can be found here).
For my thesis, I will be using the statistics environment and programming language “R” (r-project.org), and XCMS, which is a framework for mass spectra analysis. I had some trouble getting XCMS running. Hopefully, this will save someone some trouble:
On the webpage where you can download XCMS , it simply states:
To install this package, start R and enter:
You can try that, but it did not work in my case, anyway (This might just have been due to dependencies, and might have worked after the first step below, I don’t think I tested that). In any case, this is how I eventually did get it to work:
(Note: This assumes R is already installed and working. That part should go without a hitch, using e.g. the Adept installer, as the R packages are in the Ubuntu repos).
- First, get the NETcdf-library from here.
Install it as follows :
tar -xzf netcdf.tar.gz
#Replace * with version number here:
#"--prefix..." is optional # (installs in a
# directory other than the current):
sudo make install
- Now start R. To select a download-site near you, enter:
- To choose from a list of repositories, enter the following and select “BioC Software” in addition to the standard “CRAN”:
- You should now be able to find and download XCMS. To install it, enter:
That should do it! To check that you can access it, enter the following in R:
You should now see “package:xcms” somewhere in the list of active packages.
Hope this is useful to someone! 🙂