[BioC] genefilter installation error

[Martin Morgan]

On 08/22/2014 01:21 PM, Subinoy Biswas wrote:
> Please help me I am getting error while installing  genefilter package
> ** help
> *** installing help indices
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> * DONE (AnnotationDbi)
> ERROR: dependency ‘XML’ is not available for package ‘annotate’

The problem is here, the package XML is not installed, probably it failed to 
install earlier in the installation process. On Linux XML has a system 
dependency; on my system it is satisfied with

   sudo apt-get install libxml2-dev

Martin

> * removing ‘/home/subinoy/R/x86_64-pc-linux-gnu-library/3.1/annotate’
> ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
> * removing ‘/home/subinoy/R/x86_64-pc-linux-gnu-library/3.1/genefilter’
>
> The downloaded source packages are in
> ‘/tmp/RtmpFu8HQT/downloaded_packages’
> 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 ‘annotate’ had non-zero exit status
> 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>    installation of package ‘genefilter’ had non-zero exit status
> 4: installed directory not writable, cannot update packages 'codetools',
> 'MASS', 'spatial'
>> library(genefilter)
>
> Error in library(genefilter) : there is no package called ‘genefilter’
>
> 	[[alternative HTML version deleted]]
>
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