[BioC] Help in installing affycoretools

[Martin Morgan]

Sunny Srivastava wrote:
> Thanks Martin for the reply.
> 
> I am using ubuntu 9.04 and libxml2 was already installed on it. I 
> installed libcurl3 (could not find libcurl).

I am not using ubuntu; you require the 'devel' versions, for me these 
are libxml2-devel, libcurl-devel

> 
> Still I am not able to install affycoretools or XML.
> ---
>  > sessionInfo()
> R version 2.8.1 (2008-12-22)
> x86_64-pc-linux-gnu
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base    
> 
> loaded via a namespace (and not attached):
> [1] tools_2.8.1
> -----
> 
> Thanks for any help.
> 
> Regards,
> S.
> 
> On Sat, Nov 21, 2009 at 12:19 PM, Martin Morgan <mtmorgan at fhcrc.org 
> <mailto:mtmorgan at fhcrc.org>> wrote:
> 
>     Sunny Srivastava <research.baba at gmail.com
>     <mailto:research.baba at gmail.com>> writes:
> 
>      > Dear Bioconductor Helpers,
>      > I was trying to install affycoretools package on my computer but
>     it gives a
>      > series of errors and doesn't install following are the messages:
>      >
>      > ## I think the error is related to this warning at the time I use
>      > biocLite("affycoretools")
>      >
>      > Warning in install.packages(pkgs = pkgs, repos = repos,
>     dependencies =
>      > dependencies,  :
>      >   argument 'lib' is missing: using
>      > '/home/baba/R/x86_64-pc-linux-gnu-library/2.8'
>      > also installing the dependencies ‘GSEABase’, ‘Category’, ‘XML’,
>     ‘RCurl’,
>      > ‘GOstats’, ‘biomaRt’
>      >
>      > ## These are the series of errors in between downloads and other
>     gcc checks
>      >
>      > ERROR: configuration failed for package 'XML'
>      >
>      > ERROR: configuration failed for package 'RCurl'
> 
>     XML and RCurl have external operating system dependencies, likely you
>     need to install libxml2 and libcurl into your system.
> 
>     Martin
> 
>      > Error in loadNamespace(i[[1]], c(lib.loc, .libPaths())) :
>      >
>      > ERROR: lazy loading failed for package 'GSEABase'
>      >
>      > Error in loadNamespace(i, c(lib.loc, .libPaths())) :
>      >
>      > ERROR: lazy loading failed for package 'biomaRt'
>      >
>      > ERROR: lazy loading failed for package 'Category'
>      >
>      > ERROR: lazy loading failed for package 'GOstats'
>      >
>     ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>      > I also tried
>      >>biocLite("XML")
>      >
>      > But I get the same set of warnings again.
>      >
>      > Any help is appreciated.
>      >
>      >
>      > Following is my sessionInfo() output:
>      >> sessionInfo()
>      > R version 2.8.1 (2008-12-22)
>      > x86_64-pc-linux-gnu
>      >
>      > locale:
>      >
>     LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>      >
>      > attached base packages:
>      > [1] splines   tools     stats     graphics  grDevices utils    
>     datasets
>      > [8] methods   base
>      >
>      > other attached packages:
>      >  [1] mdssgpexprcdf_1.20.0 limma_2.16.5         simpleaffy_2.18.0
>      >  [4] genefilter_1.22.0    survival_2.34-1      affyPLM_1.18.1
>      >  [7] preprocessCore_1.4.0 gcrma_2.14.1         matchprobes_1.14.1
>      > [10] affy_1.20.2          Biobase_2.2.2
>      >
>      > loaded via a namespace (and not attached):
>      > [1] affyio_1.10.1       annotate_1.20.1     AnnotationDbi_1.4.3
>      > [4] DBI_0.2-4           RSQLite_0.7-3
>      >
>      >       [[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
> 
> 


-- 
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