R, biocLite, error installing DESeq2

问题

I've been trying to install DESeq2 to do some analysis for a couple days now. R and biocLite are up to date, and I'm running into permission errors when I try to run

biocLite("DESeq2")

I receive mostly good messages, but at the end I get:

1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘XML’ had non-zero exit status
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘annotate’ had non-zero exit status
3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘genefilter’ had non-zero exit status
4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘geneplotter’ had non-zero exit status
5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘DESeq2’ had non-zero exit status
>

I've tried editing permissions, running R through sudo, and adding my user to the staff group.

I'm at a loss, what else can I do to get this installed?

Thanks

回答1:

From the log, it seems that the problem originated from XML package. XML package fails to compile if libxml2 library is not available. To install it on Linux:

sudo apt-get install libxml2 
sudo apt-get install libxml2-dev

Then rerun the installation.

来源：https://stackoverflow.com/questions/28726649/r-bioclite-error-installing-deseq2

标签

bioinformatics

bioconductor