[BioC] DESeq2 dependency hell

[James W. MacDonald]

Hi Mark,

On 8/14/2013 11:57 AM, Mark Christie [guest] wrote:
> 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'

You don't show the part of the install output that is of interest, but 
it is likely that you don't have the xml headers installed. A quick look 
indicates that Mint is a Debian offshoot, so something like

sudo apt-get install libxml2-dev

should do the trick.

Best,

Jim


>
> 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
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099