[BioC] DESeq2 dependency hell
James W. MacDonald
jmacdon at uw.edu
Wed Aug 14 18:02:47 CEST 2013
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
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