Thank you very much for your replies. It worked with libxml2-dev package. Best, E.C. On 01/08/2013 03:41 PM, Wolfgang Huber wrote: > Dear Eleni > > you will need to install, at the linux level (e.g. through your distribution's package manager [1]) the xml2 system library. As a measure of success, who you type "xml2-config" on the unix shell, you should get a usage message from this program, rather "command not found". > > [1] AfaIk (others might know better) in Ubuntu, the relevant package name is "libxml2-dev". > > Best wishes > Wolfgang > > > > Il giorno Jan 8, 2013, alle ore 2:33 PM, Eleni Christodoulou [guest] <guest at="" bioconductor.org=""> ha scritto: > >> Dear Bioconductor experts, >> >> I have been working with some Bioconductor packages in R14 which I was using in the past. I recently installed R15. I upgraded the Bioconductor installation using >> source("http://bioconductor.org/biocLite.R") and >> biocLite("BiocUpgrade") >> >> I got in my terminal: >> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. >> Old packages: 'biomaRt' >> Update all/some/none? [a/s/n]: >> >> I answered a (all packages) in the last question. However, biomaRt could not be installed. Here is the error message that I received: >> checking for xml2-config... no >> Cannot find xml2-config >> ERROR: configuration failed for package ???XML??? >> * removing ???/home/cellnet/elenic/R15packages/XML??? >> ERROR: dependency ???XML??? is not available for package ???biomaRt??? >> * removing ???/home/cellnet/elenic/R15packages/biomaRt??? >> >> I thus cannot update biomaRt which is essential for my analysis. Could you provide me with some help on this? >> >> Thank you very much, >> E.C. >> >> >> >> -- output of sessionInfo(): >> >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C >> [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 >> [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] plyr_1.8 >> >> loaded via a namespace (and not attached): >> [1] tools_2.15.1 >> >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> 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 -- Eleni Christodoulou PhD student Cellular Networks Group BIOTEC TU Dresden Tatzberg 47/49 01307 Dresden, Germany phone: +49-351-463-40076 e-mail: eleni.christodoulou at biotec.tu-dresden.de