I can't install biomaRt. Is it a solution for this? I use R version 2.15.2 When i try to install biomaRt > biocLite("biomaRt") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Installing package(s) 'biomaRt' also installing the dependency 'RCurl' ... * installing *source* package 'RCurl' ... ** package 'RCurl' successfully unpacked and MD5 sums checked checking for curl-config... no Cannot find curl-config ERROR: configuration failed for package 'RCurl' * removing '/gpfs/norstore_trd/usrlocal/r/R-2.15.2/library/RCurl' ERROR: dependency 'RCurl' is not available for package 'biomaRt' * removing '/gpfs/norstore_trd/usrlocal/r/R-2.15.2/library/biomaRt' and > biocLite("Rcurl.R") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Installing package(s) 'Rcurl.R' Warning message: package 'Rcurl.R' is not available (for R version 2.15.2) John Floan Senior Engineer High Performance Computing NTNU IT Division Address: Høgskoleringen 7i NO-7491 Trondheim, Norway Mobile: +4791897646 Email: john.floan@ntnu.no [[alternative HTML version deleted]]

On Mon, Dec 17, 2012 at 3:52 AM, John Floan <john.floan@ntnu.no> wrote: > I can't install biomaRt. Is it a solution for this? > > I use R version 2.15.2 > When i try to install biomaRt > > biocLite("biomaRt") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. > Installing package(s) 'biomaRt' > also installing the dependency 'RCurl' > ... > * installing *source* package 'RCurl' ... > ** package 'RCurl' successfully unpacked and MD5 sums checked > checking for curl-config... no > Cannot find curl-config > Hi, John. Note that you need to install libcurl and libcurl-devel for your platform, which is, I am guessing, linux-based. See SystemRequirements on this page: http://cran.r-project.org/web/packages/RCurl/index.html After that, biocLite('RCurl') should install RCurl. Sean > ERROR: configuration failed for package 'RCurl' > * removing '/gpfs/norstore_trd/usrlocal/r/R-2.15.2/library/RCurl' > ERROR: dependency 'RCurl' is not available for package 'biomaRt' > * removing '/gpfs/norstore_trd/usrlocal/r/R-2.15.2/library/biomaRt' > > > and > > > biocLite("Rcurl.R") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. > Installing package(s) 'Rcurl.R' > Warning message: > package 'Rcurl.R' is not available (for R version 2.15.2) > > > > > > > John Floan > Senior Engineer > High Performance Computing > NTNU IT Division > Address: > Høgskoleringen 7i > NO-7491 Trondheim, Norway > Mobile: +4791897646 > Email: john.floan@ntnu.no > > [[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 > [[alternative HTML version deleted]]

Dear John yes, you need to install the system library 'curl' on your computer. As a control of success, when you type 'curl-config' on the operating system command line (this is different from the R prompt), you should get a usage message from this programme. If these remarks mean not much to you, then best contact your system administrator. Best wishes Wolfgang Il giorno Dec 17, 2012, alle ore 9:52 AM, John Floan <john.floan at="" ntnu.no=""> ha scritto: > I can't install biomaRt. Is it a solution for this? > > I use R version 2.15.2 > When i try to install biomaRt >> biocLite("biomaRt") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. > Installing package(s) 'biomaRt' > also installing the dependency 'RCurl' > ... > * installing *source* package 'RCurl' ... > ** package 'RCurl' successfully unpacked and MD5 sums checked > checking for curl-config... no > Cannot find curl-config > ERROR: configuration failed for package 'RCurl' > * removing '/gpfs/norstore_trd/usrlocal/r/R-2.15.2/library/RCurl' > ERROR: dependency 'RCurl' is not available for package 'biomaRt' > * removing '/gpfs/norstore_trd/usrlocal/r/R-2.15.2/library/biomaRt' > > > and > >> biocLite("Rcurl.R") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. > Installing package(s) 'Rcurl.R' > Warning message: > package 'Rcurl.R' is not available (for R version 2.15.2) > > > > > > > John Floan > Senior Engineer > High Performance Computing > NTNU IT Division > Address: > H?gskoleringen 7i > NO-7491 Trondheim, Norway > Mobile: +4791897646 > Email: john.floan at ntnu.no > > [[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