I’m switching computer again, and as usual this is the moment I chose to upgrade the pieces of software which are the most painful to upgrade, ie, in my case, most notably C++ libraries such as Boost, the C++ compiler (GCC 4.6, hurray! ) and R (R-project) because of the need to reinstall all the extra packages (provided that the packages got updated in the first place!).
I never kept track of where I got my package from (CRAN vs Bioconductor) – in the future I’ll be more careful. Anyway, I encountered a weird issue when getting the Bioconductor packages:
Error in file(file, "r", encoding = encoding) :
cannot open the connection
In addition: Warning message:
In file(file, "r", encoding = encoding) :
InternetOpenUrl failed: 'The URL is invalid'
Indeed I thought that URL looked fishy. I’m not sure I remember whether or not it used to work (I don’t see how it possibly could, though), but at least at the moment it doesn’t.
A quick search for “source(“http:///biocLite.R”) not wokring” briefly got me the solution: the proper URL is http://bioconductor.org/biocLite.R, not http://biocLite.R.
So, whichever Bioconductor package you’re installing, the magic lines are:
biocLite("[package name here]")