biomaRt installation error ??
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Alyaa Mahmoud ▴ 440
@alyaa-mahmoud-4670
Last seen 19 months ago
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]]
biomaRt biomaRt • 3.4k views
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@david-westergaard-5119
Last seen 7.1 years ago
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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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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 [[alternative HTML version deleted]]
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