[BioC] Help in installing affycoretools

[Martin Morgan]

Sunny Srivastava <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
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