[BioC] installation packages

[Steve Lianoglou]

Hi Fran,

Please keep all emails on list (hit "reply-all") so that your emails go back to the main bioconductor list as well.

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Now:

> I performed this command and I solved the problem only for installation of XML packages, because if I try to perform biocLite for the other packages it results:
> Warning messages:
> 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>   installation of package ‘rtracklayer’ had non-zero exit status
> 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>   installation of package ‘GenomicFeatures’ had non-zero exit status
> 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>   installation of package ‘VariantAnnotation’ had non-zero exit status
> 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>   installation of package ‘gmapR’ had non-zero exit status
> 
> This is the same warning message that I had with XML packages. How I can solve it?

You will need to provide more output than that to get help.

You say that after installing libcurl-dev and libxml2-dev on your system, the  XML library install worked in R?

So when you do `library(XML)` inside R, does it load properly?

Can you please provide the entire output when you do:

R> library(BiocInstaller)
R> biocLite(c("RCurl", "rtracklayer"))

Please also include the entire output of sessionInfo() after the above commands fail.

Thanks,
-steve

--
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech