[BioC] DESeq2 dependency hell

[Mark Christie [guest]]

Hi all,

I have entered dependency hell when trying to install DESEq2.  I am using Rstudio that is running on linux Mint, with R version 3.0.1.  

When I run biocLite(c("DESeq2"), dependencies = TRUE), I get the following warnings at the end of what almost seems like a successful install (See below).  I don't think this problem is specific to DESeq2, but does anybody have an idea as to what is going on here.

Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package ‘RCurl’ had non-zero exit status
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package ‘XML’ had non-zero exit status
3: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package ‘biomaRt’ had non-zero exit status
4: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package ‘annotate’ had non-zero exit status
5: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package ‘geneplotter’ had non-zero exit status
6: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package ‘DEXSeq’ had non-zero exit status
7: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package ‘genefilter’ had non-zero exit status
8: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package ‘DESeq’ had non-zero exit status
9: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package ‘DESeq2’ had non-zero exit status
10: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package ‘pasilla’ had non-zero exit status
11: installed directory not writable, cannot update packages 'MASS', 'spatial'

Many Thanks!

Mark Christie

 -- output of sessionInfo(): 

R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.10.3

loaded via a namespace (and not attached):
[1] tools_3.0.1

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