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[R] How to fix package installation failure on “checking for xml2-config”

I’ve recently had to set up a secondary computation server running R-project. Unfortunately, like all my servers, it runs under Linux, and R is a PITA to run under Linux. Notably, packages must be compiled on the machine: not only this is long, but also it requires tons of programming-related dependencies (GCC and such), and, well, it tends to fail sometimes.

While I’m at it, here are the repositories to be added to /etc/apt/sources.list in Debian 7:

deb http://mirrors.softliste.de/cran/bin/linux/debian wheezy-cran3/
deb-src http://mirrors.softliste.de/cran/bin/linux/debian wheezy-cran3/

So, I wanted to install a few packages from Bioconductor, notably the “GOSim” package. But installation failed on the “XML” package dependency (yes, it’s a package named “XML”), with the following apparent issues:
checking for pkg-config... no
checking for xml2-config... no

So apparently, some dependencies were missing despite that infamous package manager system which I seem to be the only one to hate. The first dependency was trivial to fix:
apt-get install pkg-config
But for the second one, that trick didn’t work.

I eventually found on some Stackoverflow page that the relevant package is libxml2-dev, so:
apt-get install libxml2-dev

And that’s it, you should now be able to install your package… or move to the next missing dependency :-p

Posted in R (R-project).


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