Thanks for sharing your expertise Jim - that solution worked perfectly!


On Wed, Aug 14, 2013 at 12:02 PM, James W. MacDonald <jmacdon@uw.edu> wrote:

> 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
>
>


-- 
Mark R. Christie, PhD
Department of Zoology,
Oregon State University
http://www.science.oregonstate.edu/~christim/

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