Hi David

Thanks a lot for pointing this out. the same problem was for the XML
package.

sudo apt-get install libxml2-dev

sudo apt-get install libcurl4-openssl-dev

Thanks again
yours,
Alyaa

On Sat, Jun 16, 2012 at 1:42 PM, David Westergaard <david@harsk.dk> wrote:

> 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@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]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>



-- 
Alyaa Mahmoud

"Love all, trust a few, do wrong to none"- Shakespeare

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