mauede at alice.it
2010-May-31 12:03 UTC
[R] after updating biomaRt cannot connect any more
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]]
Heidi Dvinge
2010-May-31 12:28 UTC
[R] [BioC] after updating biomaRt cannot connect any more
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 31.05.2010 14:03, 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. > > 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 ?1. If you upgraded, why to R-2.10.1. given R-2.11.1 has been released today? Hence my recommedndation is to go ahead for R-2.11.1 2. After strating R say update.packages(checkBuilt=TRUE) and all your outdated packages will be updated for the current version of R. Uwe Ligges> Thank you in advance. > Maura > > > > > > > > tutti i telefonini TIM! > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at 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.
Sean Davis
2010-May-31 21:21 UTC
[R] [BioC] after updating biomaRt cannot connect any more
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]]