Provided you have installed R-devel and the necessary infrastructure as
noted by Martin, and properly installed the appropriate biocLite utility
with

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

you should proceed with biocLite, which will resolve all dependencies.  I
suspect you are trying to install the package that you downloaded as
source, manually, using R CMD INSTALL.  biocLite is provided to resolve the
dependencies.  [Note, in the transcript below, only a few packages are
added to the request because I have already installed a number of the
dependencies for other purposes.]


> biocLite("SomaticSignatures")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.14 (BiocInstaller 1.13.3), R version 3.1.0.
Installing package(s) 'SomaticSignatures'
also installing the dependencies 'gridBase', 'NMF', 'pcaMethods'

trying URL 'http://cran.fhcrc.org/src/contrib/gridBase_0.4-7.tar.gz'
Content type 'application/x-gzip' length 153373 bytes (149 Kb)
opened URL
==================================================
downloaded 149 Kb

trying URL 'http://cran.fhcrc.org/src/contrib/NMF_0.20.5.tar.gz'
Content type 'application/x-gzip' length 1763782 bytes (1.7 Mb)
opened URL
==================================================
downloaded 1.7 Mb

trying URL '
http://bioconductor.org/packages/2.14/bioc/src/contrib/pcaMethods_1.53.4.tar.gz
'
Content type 'application/x-gzip' length 714560 bytes (697 Kb)
opened URL
==================================================



On Thu, Mar 27, 2014 at 4:01 PM, Huma Asif <humaasif79@yahoo.com> wrote:

> Hi
> Though i installed variant annotation and R vesion as suggested. every
> package seems dependent on other like somatic
> signature....mutationcontext..... variantannotation......GRanges....h5vc
> package.
> It seems impossible
> I need  to know is there any other package that can help in signatures
> extraction from vcf files with out being dependent on R.
> Regards
>
>
>
> >________________________________
> > From: Martin Morgan <mtmorgan@fhcrc.org>
> >To: Huma Asif <humaasif79@yahoo.com>; Steve Lianoglou <
> lianoglou.steve@gene.com>
> >Cc: "bioconductor@r-project.org list" <bioconductor@r-project.org>
> >Sent: Tuesday, March 25, 2014 5:24 PM
> >Subject: Re: [BioC] SomaticSignatures
> >
> >
> >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@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
> >
> >>
> >>
> >>
> >
> >
> >--
> >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
> >
> >
> >
>         [[alternative HTML version deleted]]
>
>
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