Some Interesting R Library Quirks
Submitted by lev_lafayette on Sun, 09/06/2015 - 12:17
A researcher uses an HPC system to analyse DNA methylation data. However when they try to install some related libraries, the installation fails. The packages in question are minfi, IlluminaHumanMethylation450kmanifest, and FlowSorted.Blood.450k.
Initially, it was suggested that one of the more recent versions of R should be used for these libraries. However, when an installation was attempted on 3.1.2, it failed. Moving backwards, to R version 2.15, installation also failed. In between the two extreme versions one (R/3.0.3-gcc) did succeed.
There are two lessons from this. The first is (a) thank goodness for environment modules that allow for installations for such crazy situations and (b) software libraries sometimes require the latest version of an application and sometime have been abandoned and require an older version. It is a real problem however when there is a only window of opportunity for a library to work.