[R] problems in installing biomart

Martin Morgan mtmorgan at fhcrc.org
Wed Nov 11 17:12:18 CET 2009


Hi Andreia --

Andreia Fonseca wrote:
> Dear Forum
> 
> my machine runs Ubuntu 9.04. I am trying to install Biomart, what I realize
> is that something is missing and it can't install XML, RCurl but I don't
> know what more to do, I looked in previous posts but I did not find
> infoprmation that helped.
> Thanks
> Andreia
> biocLite("biomaRt")
> Running biocinstall version 2.3.14 with R version 2.8.1
> Your version of R requires version 2.3 of Bioconductor.
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>   argument 'lib' is missing: using
> '/home/user/R/x86_64-pc-linux-gnu-library/2.8'
> also installing the dependencies ‘XML’, ‘RCurl’
> 
> trying URL 'http://cran.fhcrc.org/src/contrib/XML_2.6-0.tar.gz'
> Content type 'application/x-gzip' length 680366 bytes (664 Kb)
> opened URL
> ==================================================
> downloaded 664 Kb
> 
> trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.3-0.tar.gz'
> Content type 'application/x-gzip' length 799689 bytes (780 Kb)
> opened URL
> ==================================================
> downloaded 780 Kb
> 
> trying URL '
> http://bioconductor.org/packages/2.3/bioc/src/contrib/biomaRt_1.16.0.tar.gz'
> Content type 'application/x-gzip' length 278561 bytes (272 Kb)
> opened URL
> ==================================================
> downloaded 272 Kb
> 
> * Installing *source* package 'XML' ...
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ANSI C... none needed
> checking how to run the C preprocessor... gcc -E
> checking for sed... /bin/sed
> checking for pkg-config... /usr/bin/pkg-config
> checking for xml2-config... no
> Cannot find xml2-config
> ERROR: configuration failed for package 'XML'

use your operating system package installation manager to install libxml2.

This is a Bioconductor package, so consider asking on the Biocondcutor
mailing list.

Martin

> ** Removing '/home/user/R/x86_64-pc-linux-gnu-library/2.8/XML'
> * Installing *source* package 'RCurl' ...
> checking for curl-config... no
> Cannot find curl-config
> ERROR: configuration failed for package 'RCurl'
> ** Removing '/home/user/R/x86_64-pc-linux-gnu-library/2.8/RCurl'
> * Installing *source* package 'biomaRt' ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Error in loadNamespace(i, c(lib.loc, .libPaths())) :
>   there is no package called 'RCurl'
> Calls: <Anonymous> ... code2LazyLoadDB -> loadNamespace -> namespaceImport
> -> loadNamespace
> Execution halted
> ERROR: lazy loading failed for package 'biomaRt'
> ** Removing '/home/user/R/x86_64-pc-linux-gnu-library/2.8/biomaRt'
> 
> The downloaded packages are in
>     /tmp/RtmpzdpweV/downloaded_packages
> Warning messages:
> 1: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>   installation of package 'XML' had non-zero exit status
> 2: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>   installation of package 'RCurl' had non-zero exit status
> 3: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>   installation of package 'biomaRt' had non-zero exit status
> 
> 	[[alternative HTML version deleted]]
> 
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
Martin Morgan
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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