[BioC] biomaRt installation error ??

[David Westergaard]

Dear Alyaa,

It seems your problem is related to RCurl, and not the biomaRt
package. A quick google search on 'Cannot find curl-config' seems to
return a very relevant hit: http://www.omegahat.org/RCurl/FAQ.html
Could you try this, and then try installing RCurl again?

Best,
David



2012/6/16 Alyaa Mahmoud <alyamahmoud at gmail.com>:
> Hi All
>
> I am having a problem installing biomaRt. Did the package names change or
> sth ??
>
> I install biomart normally from biocLite
> source ("http://bioconductor.org/biocLite)
> biocLite ("biomaRt")
>
> but I get this erros (XML and RCurl):
>
> ERROR: configuration failed for package 'XML'
> * removing '/home/alyaa/R/x86_64-pc-linux-gnu-library/2.11/XML'
> During startup - Warning message:
> Setting LC_CTYPE failed, using "C"
> * installing *source* package 'RCurl' ...
> checking for curl-config... no
> Cannot find curl-config
> ERROR: configuration failed for package 'RCurl'
> * removing '/home/alyaa/R/x86_64-pc-linux-gnu-library/2.11/RCurl'
> During startup - Warning message:
> Setting LC_CTYPE failed, using "C"
> ERROR: dependencies 'XML', 'RCurl' are not available for package 'biomaRt'
>
> I then try to install RCurl or XML independently, but I get the same error:
>
> ERROR: configuration failed for package 'RCurl'
> * removing '/home/alyaa/R/x86_64-pc-linux-gnu-library/2.11/RCurl'
>
> The downloaded packages are in
> '/tmp/Rtmp6dsDAX/downloaded_packages'
> Warning message:
> In install.packages("RCurl") :
>  installation of package 'RCurl' had non-zero exit status
>
> I was using biomart normally 3-4 months ago so I am not sure if sth has
> been updated or so ?? any ideas ?
>
> Thanks a lot
> Alyaa
> --
> Alyaa Mahmoud
>
> "Love all, trust a few, do wrong to none"- Shakespeare
>
>        [[alternative HTML version deleted]]
>
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