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. 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 ? Thank you in advance. Maura tutti i telefonini TIM! [[alternative HTML version deleted]]

On 31 May 2010, at 13:03, <mauede at="" alice.it=""> <mauede at="" 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. > Did you check this as suggested in the error message? Currently, when I try http://www.biomart.org/ it doesn't seem to work. Regards \Heidi > 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 ? > > Thank you in advance. > Maura > > > > > > > > tutti i telefonini TIM! > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor

On Mon, May 31, 2010 at 8:03 AM, <mauede@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]]