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Solving the invalid source for Bioconductor packages

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:
source("http:///biocLite.R")
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:
source("http://bioconductor.org/biocLite.R")
biocLite("[package name here]")

Posted in R (R-project).


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