Hi,
i am using Ubuntu 12.04 on VM wareplayer
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yes i downloaded source package 
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 i have installed some of the packages that are required for Somaticsignature however i need  help with these error during variantannotation installation


source("http://bioconductor.org/biocLite.R")
> biocLite()

Biobase' 'IRanges' 'AnnotationDbi' also installing the dependencies ‘BiocGenerics’, ‘DBI’, ‘RSQLite’ 
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ERRORS during varriant annotation
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ERROR: configuration failed for package ‘XML’
 removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.0/XML’


Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.0/RCurl’

ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘biomaRt’
* removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.0/biomaRt’

samtools/bgzf.h:33:18: fatal error: zlib.h: No such file or directory
compilation terminated.
make: *** [R_init_Rsamtools.o] Error 1
ERROR: compilation failed for package ‘Rsamtools’
* removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.0/Rsamtools’

ERROR: dependencies ‘XML’, ‘RCurl’, ‘Rsamtools’ are not available for package ‘rtracklayer’
* removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.0/rtracklayer’
ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘RCurl’ are not available for package ‘GenomicFeatures’
* removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.0/GenomicFeatures’
ERROR: dependencies ‘Rsamtools’, ‘GenomicFeatures’, ‘rtracklayer’ are not available for package 

‘VariantAnnotation’
* removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.0/VariantAnnotation’


Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘XML’ had non-zero exit status
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘RCurl’ 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 ‘Rsamtools’ had non-zero exit status
5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘rtracklayer’ had non-zero exit status
6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘GenomicFeatures’ had non-zero exit status
7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘VariantAnnotation’ had non-zero exit status


i am planning to install  R-3.1.0 alpha and removing the current R version
please give me the link for this R version


Do you think the packages installed will work with R-3.1.0 alpha
confused








Regards
Huma


>________________________________
> From: Martin Morgan <mtmorgan@fhcrc.org>
>To: Steve Lianoglou <lianoglou.steve@gene.com>; Huma Asif <humaasif79@yahoo.com> 
>Cc: "bioconductor@r-project.org list" <bioconductor@r-project.org> 
>Sent: Monday, March 24, 2014 4:44 PM
>Subject: Re: [BioC] SomaticSignatures
> 
>
>On 03/24/2014 12:12 PM, Steve Lianoglou wrote:
>> If you insist on installing this package into your current working version of R
>> (after you installed the dependent packages), you may be able to do so if it
>> doesn't depend on functionality coming in bioc2.14 that's not in bioc2.13 -- I
>> have no idea of knowing the answer to that.
>
>Do not try to install a 'devel' version into your current R version.
>
>
>>
>> If I were you, I'd install a working version of R-devel and all of the packages
>> from bioc2.14 -- which will happen automatically when  you use biocLite.
>>
>
>Not R-devel, but R-3.1.0 alpha, followed by the installation instructions on the 
>SomaticSignatures developer landing page. Do not attempt anything more elaborate.
>
>Martin
>
>-- 
>Computational Biology / Fred Hutchinson Cancer Research Center
>1100 Fairview Ave. N.
>PO Box 19024 Seattle, WA 98109
>
>Location: Arnold Building M1 B861
>Phone: (206) 667-2793
>
>
>
>
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