solving DESeq2 installation issues

At work a colleague asked me to do a system-wide installation of the R module DESeq2 in one of our internal servers.
The installation procedure is quite straight-forward:

source("http://bioconductor.org/biocLite.R")
biocLite("DESeq2")

Unfortunately I had some issues on my system, in fact I got:

…
Warning in fun(libname, pkgname) :
couldn't connect to display "localhost:12.0"
* DONE (maSigPro)

The downloaded source packages are in
	‘/tmp/RtmpfdD2RC/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘XML’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘annotate’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘genefilter’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘geneplotter’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘DESeq2’ had non-zero exit status

I then tried to install manually the various dependencies, like XML. Still no luck. After a quick Google search I found that I was missing a couple of -dev packages on my Ubuntu machine, so I installed them:

root@server:~# apt-get install libcurl4-openssl-dev libxml2-dev

… and then re-tried to install DESeq2.
This time everything was ok! Problem solved!

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Author: kOoLiNuS

♂, Italian, male, husband, dad of a wonder, “cazzaro”, friendly, blogger, motorcyclist, geek, avid reader, sysadmin, ICT consultant, curious. I come in peace… I'm an active social networker since 1999. I've been using WordPress sice 2004 and WordPress.com since 2006, and I'm currently involved in WordPress and WooCommerce communities in Bari, Apulia.

One thought on “solving DESeq2 installation issues”

  1. Than’ks a lot!!!!! I spent almost two hours trying to figure out how to fix this problem with xml and the forums were helpless, your solution was quite precise.

    greetings from Brazil.

    Liked by 1 person

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