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Question: Problems with biomaRt
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gravatar for michael watson IAH-C
9.1 years ago by
michael watson IAH-C3.4k wrote:
I'm having problems connecting to biomaRt through R. useMart reports an error and claims either the service is down or I am not connected to the internet: > mart <- useMart(biomart="ensembl", dataset="ggallus_gene_ensembl") 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. But R can connect to martservice just fine: > download.file(url="http://www.biomart.org/biomart/martservice", destfile="test.html") trying URL 'http://www.biomart.org/biomart/martservice' Content type 'text/plain' length 200 bytes opened URL downloaded 5810 bytes So the problem is not R, it is biomaRt. Any help appreciated Mick > sessionInfo() R version 2.9.1 (2009-06-26) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] CORNA_1.1 XML_2.5-3 GEOquery_2.8.0 RCurl_0.98-1 bitops_1.0-4.1 biomaRt_2.0.0 Biobase_2.4.1 Head of Bioinformatics Institute for Animal Health Compton Berks RG20 7NN 01635 578411 Please consider the environment and don't print this e-mail unless you really need to. The information contained in this message may be confide...{{dropped:26}}
ADD COMMENTlink modified 9.1 years ago by john seers IFR810 • written 9.1 years ago by michael watson IAH-C3.4k
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gravatar for James W. MacDonald
9.1 years ago by
United States
James W. MacDonald47k wrote:
It's working for me: > library(biomaRt) > mart <- useMart("ensembl","hsapiens_gene_ensembl") Checking attributes ... ok Checking filters ... ok > sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] biomaRt_2.0.0 loaded via a namespace (and not attached): [1] RCurl_0.98-1 XML_2.5-1 > Sys.time() [1] "2009-07-13 09:17:58 EDT" Maybe try again? Best, Jim michael watson (IAH-C) wrote: > I'm having problems connecting to biomaRt through R. > > > > useMart reports an error and claims either the service is down or I am > not connected to the internet: > > > >> mart <- useMart(biomart="ensembl", dataset="ggallus_gene_ensembl") > > 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. > > > > But R can connect to martservice just fine: > > > >> download.file(url="http://www.biomart.org/biomart/martservice", > destfile="test.html") > > trying URL 'http://www.biomart.org/biomart/martservice' > > Content type 'text/plain' length 200 bytes > > opened URL > > downloaded 5810 bytes > > > > So the problem is not R, it is biomaRt. > > > > Any help appreciated > > > > Mick > > > >> sessionInfo() > > R version 2.9.1 (2009-06-26) > > i386-pc-mingw32 > > > > locale: > > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > > > attached base packages: > > [1] tools stats graphics grDevices utils datasets methods > base > > > > other attached packages: > > [1] CORNA_1.1 XML_2.5-3 GEOquery_2.8.0 RCurl_0.98-1 > bitops_1.0-4.1 biomaRt_2.0.0 Biobase_2.4.1 > > > > Head of Bioinformatics > Institute for Animal Health > Compton > Berks > RG20 7NN > 01635 578411 > > > > Please consider the environment and don't print this e-mail unless you > really need to. > > The information contained in this message may be confide...{{dropped:26}} > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826
ADD COMMENTlink written 9.1 years ago by James W. MacDonald47k
It is for me now, only I had to add: Sys.setenv("http_proxy"="http://wwwcache.bbsrc.ac.uk:8080") I didn't have to do this previously, and obviously R knows about my proxy as it can use download.file (I am using the --internet2 switch to get connection settings from IE). Does biomaRt not use the proxy settings in some way that download.file does? Clearly this is not a huge problem as I can simply add "Sys.setenv("http_proxy"="http://wwwcache.bbsrc.ac.uk:8080")" to all my scripts, but this wasn't the case previously and I expect biomaRt should be smart enough to pick up my proxy settings... -----Original Message----- From: James W. MacDonald [mailto:jmacdon@med.umich.edu] Sent: 13 July 2009 14:19 To: michael watson (IAH-C) Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Problems with biomaRt It's working for me: > library(biomaRt) > mart <- useMart("ensembl","hsapiens_gene_ensembl") Checking attributes ... ok Checking filters ... ok > sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] biomaRt_2.0.0 loaded via a namespace (and not attached): [1] RCurl_0.98-1 XML_2.5-1 > Sys.time() [1] "2009-07-13 09:17:58 EDT" Maybe try again? Best, Jim michael watson (IAH-C) wrote: > I'm having problems connecting to biomaRt through R. > > > > useMart reports an error and claims either the service is down or I am > not connected to the internet: > > > >> mart <- useMart(biomart="ensembl", dataset="ggallus_gene_ensembl") > > 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. > > > > But R can connect to martservice just fine: > > > >> download.file(url="http://www.biomart.org/biomart/martservice", > destfile="test.html") > > trying URL 'http://www.biomart.org/biomart/martservice' > > Content type 'text/plain' length 200 bytes > > opened URL > > downloaded 5810 bytes > > > > So the problem is not R, it is biomaRt. > > > > Any help appreciated > > > > Mick > > > >> sessionInfo() > > R version 2.9.1 (2009-06-26) > > i386-pc-mingw32 > > > > locale: > > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > > > attached base packages: > > [1] tools stats graphics grDevices utils datasets methods > base > > > > other attached packages: > > [1] CORNA_1.1 XML_2.5-3 GEOquery_2.8.0 RCurl_0.98-1 > bitops_1.0-4.1 biomaRt_2.0.0 Biobase_2.4.1 > > > > Head of Bioinformatics > Institute for Animal Health > Compton > Berks > RG20 7NN > 01635 578411 > > > > Please consider the environment and don't print this e-mail unless you > really need to. > > The information contained in this message may be confide...{{dropped:26}} > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826
ADD REPLYlink written 9.1 years ago by michael watson IAH-C3.4k
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gravatar for john seers IFR
9.1 years ago by
john seers IFR810 wrote:
Hi I had similar problems which I raised in this forum a month or so ago. The solution was, I think, to specify both the "--internet2" and the "http_proxy" options on the command line. It appears that just the one option is not sufficient for bioMart and one of the packages it uses (RCurl?). The two packages must handle the proxy slightly differently. Regards John -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of michael watson (IAH-C) Sent: 13 July 2009 14:11 To: bioconductor at stat.math.ethz.ch Subject: [BioC] Problems with biomaRt I'm having problems connecting to biomaRt through R. useMart reports an error and claims either the service is down or I am not connected to the internet: > mart <- useMart(biomart="ensembl", dataset="ggallus_gene_ensembl") 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. But R can connect to martservice just fine: > download.file(url="http://www.biomart.org/biomart/martservice", destfile="test.html") trying URL 'http://www.biomart.org/biomart/martservice' Content type 'text/plain' length 200 bytes opened URL downloaded 5810 bytes So the problem is not R, it is biomaRt. Any help appreciated Mick > sessionInfo() R version 2.9.1 (2009-06-26) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] CORNA_1.1 XML_2.5-3 GEOquery_2.8.0 RCurl_0.98-1 bitops_1.0-4.1 biomaRt_2.0.0 Biobase_2.4.1 Head of Bioinformatics Institute for Animal Health Compton Berks RG20 7NN 01635 578411 Please consider the environment and don't print this e-mail unless you really need to. The information contained in this message may be\ confid...{{dropped:10}}
ADD COMMENTlink written 9.1 years ago by john seers IFR810
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