[BioC] SomaticSignatures

[Martin Morgan]

On 03/25/2014 01:08 PM, Huma Asif wrote:
> Hi,
> i am using Ubuntu 12.04 on VM wareplayer
> XXXXXXXXXXXXXXXXXXXXXXXXXXX
> yes i downloaded source package
> XXXXXXXXXXXXXXXXXXXXXX
>
>   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’
> XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> ERRORS during varriant annotation
> XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> ........................................................
> 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’

These are missing system (instead of R) dependencies; you'll need (be sure to 
get the 'dev' versions)

   sudo apt-get install libxml2-dev
   sudo apt-get install libcurl4-openssl-dev

>
> samtools/bgzf.h:33:18: fatal error: zlib.h: No such file or directory

This is surprising, suggesting that you have a very minimal system. You'll need

   sudo apt-get install zlib1g-dev

I am not sure of the precise library versions.

Martin

> 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 at fhcrc.org>
>     *To:* Steve Lianoglou <lianoglou.steve at gene.com>; Huma Asif
>     <humaasif79 at yahoo.com>
>     *Cc:* "bioconductor at r-project.org list" <bioconductor at 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
>
>
>


-- 
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