On Mon, May 31, 2010 at 8:03 AM, <mau...@alice.it> wrote: > I recently updated R 2.10.1 Patched (2010-02-20 r51163) > This morning I reinstalled biomaRt using biocLite. > Now I can no more connect to biomaRt and even the following instruction is > hanging for a while until > the same error message pops up. > > listMarts() > Error in value[[3L]](cond) : > Request to BioMart web service failed. Verify if you are still connected > to the internet. Alternatively the BioMart web service is temporarily down. > > As Heidi suggested, how did you check to see if you were connected to the internet? And was the BioMart service up and how did you check?
> I checked my command syntax and got the following message: > > library(help=biomaRt) > Warning messages: > 1: package 'JavaGD' was built under R version 2.9.0 and help may not work > correctly > 2: package 'Biobase' was built under R version 2.9.0 and help may not work > correctly > 3: package 'Biostrings' was built under R version 2.9.0 and help may not > work correctly > 4: package 'IRanges' was built under R version 2.9.0 and help may not work > correctly > 5: package 'CORNA' was built under R version 2.9.0 and help may not work > correctly > 6: package 'GEOquery' was built under R version 2.9.0 and help may not work > correctly > 7: package 'microRNA' was built under R version 2.9.0 and help may not work > correctly > 8: package 'Rlibstree' was built under R version 2.9.0 and help may not > work correctly > > > I am stuck. > Which packages am I supposed to install again ? Maybe shall I get rid of R > 2.10.1 Patched > and restart from scratch ? > > Read this page. http://bioconductor.org/docs/install/ If you have problems after following the instructions, please follow the instructions in the posting guide and ask your question again. Also, note that the newest version of R is 2.11 and not 2.10.1 Patched. Sean [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
