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Question: biomaRt problem
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gravatar for Dario Greco
12.2 years ago by
Dario Greco310
Dario Greco310 wrote:
dear list, i am trying to annotate some genes using biomaRt, but i am running in the following problem: > library(biomaRt) Loading required package: XML Loading required package: RCurl > mart <- useMart("ensembl") Error in curlPerform(curl = curl, .opts = opts) : Couldn't resolve host 'www.biomart.org' i have also updated to the 1.7.6 version of biomaRt, but no change in the result. > sessionInfo() Version 2.3.1 (2006-06-01) i686-redhat-linux-gnu attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" [7] "base" other attached packages: biomaRt RCurl XML "1.7.6" "0.6-2" "0.99-8" i am pretty sure my computer doesn't have any proxy issues. moreover, if i try to open the www.biomart.org website in my browser, it appears down. is there some problem with the biomart mirror? should i use an alternative host? if yes, which? do you have any other suggestions? thanks in advance for your kind help. sincerely Dario -- Dario Greco Institute of Biotechnology - University of Helsinki Building Cultivator II P.O.Box 56 Viikinkaari 4 FIN-00014 Finland Office: +358 9 191 58951 Fax: +358 9 191 58952 Mobile: +358 44 023 5780
ADD COMMENTlink modified 12.2 years ago by Steffen Durinck580 • written 12.2 years ago by Dario Greco310
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gravatar for Steffen Durinck
12.2 years ago by
Steffen Durinck580 wrote:
Hi Dario, Yes it looks like the website has been down for a few days which explains why useMart fails. I've CC'd Arek (BioMart developer) maybe he can shed more light on what is happening. best. Steffen -----Original Message----- From: Dario Greco [mailto:dario.greco@helsinki.fi] Sent: Tue 8/22/2006 4:59 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] biomaRt problem dear list, i am trying to annotate some genes using biomaRt, but i am running in the following problem: > library(biomaRt) Loading required package: XML Loading required package: RCurl > mart <- useMart("ensembl") Error in curlPerform(curl = curl, .opts = opts) : Couldn't resolve host 'www.biomart.org' i have also updated to the 1.7.6 version of biomaRt, but no change in the result. > sessionInfo() Version 2.3.1 (2006-06-01) i686-redhat-linux-gnu attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" [7] "base" other attached packages: biomaRt RCurl XML "1.7.6" "0.6-2" "0.99-8" i am pretty sure my computer doesn't have any proxy issues. moreover, if i try to open the www.biomart.org website in my browser, it appears down. is there some problem with the biomart mirror? should i use an alternative host? if yes, which? do you have any other suggestions? thanks in advance for your kind help. sincerely Dario -- Dario Greco Institute of Biotechnology - University of Helsinki Building Cultivator II P.O.Box 56 Viikinkaari 4 FIN-00014 Finland Office: +358 9 191 58951 Fax: +358 9 191 58952 Mobile: +358 44 023 5780 _______________________________________________ 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
ADD COMMENTlink written 12.2 years ago by Steffen Durinck580
hi Steffen, thanks for your help. now biomart.org is up, but there are still some problems. > mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") Error in file(file, "r") : unable to open connection In addition: Warning message: unable to resolve 'web50-node4.ebi.ac.uk'. and in fact, if i try to open in browser the address http://www.biomart.org/biomart/martservice i get this internal error message: <html><head> 200 OK </head><body>

OK

The server encountered an internal error or misconfiguration and was unable to complete your request.

Please contact the server administrator, webmaster&#064;mydomain.org and inform them of the time the error occurred, and anything you might have done that may have caused the error.

More information about this error may be available in the server error log.

</body></html> what to do? thanks again for your kind help sincerely Dario On Tuesday 22 August 2006 15:58, Durinck, Steffen (NIH/NCI) [F] wrote: > Hi Dario, > > Yes it looks like the website has been down for a few days which explains > why useMart fails. I've CC'd Arek (BioMart developer) maybe he can shed > more light on what is happening. > > best. > Steffen > > > -----Original Message----- > From: Dario Greco [mailto:dario.greco at helsinki.fi] > Sent: Tue 8/22/2006 4:59 AM > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] biomaRt problem > > dear list, > i am trying to annotate some genes using biomaRt, but i am running in the > > following problem: > > library(biomaRt) > > Loading required package: XML > Loading required package: RCurl > > > mart <- useMart("ensembl") > > Error in curlPerform(curl = curl, .opts = opts) : > Couldn't resolve host 'www.biomart.org' > > i have also updated to the 1.7.6 version of biomaRt, but no change in the > result. > > > sessionInfo() > > Version 2.3.1 (2006-06-01) > i686-redhat-linux-gnu > > attached base packages: > [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" > [7] "base" > > other attached packages: > biomaRt RCurl XML > "1.7.6" "0.6-2" "0.99-8" > > i am pretty sure my computer doesn't have any proxy issues. moreover, if i > try to open the www.biomart.org website in my browser, it appears down. is > there some problem with the biomart mirror? should i use an alternative > host? if yes, which? > do you have any other suggestions? > thanks in advance for your kind help. > sincerely > Dario -- Dario Greco Institute of Biotechnology - University of Helsinki Building Cultivator II P.O.Box 56 Viikinkaari 4 FIN-00014 Finland Office: +358 9 191 58951 Fax: +358 9 191 58952 Mobile: +358 44 023 5780

ADD REPLYlink written 12.2 years ago by Dario Greco310
Hi Dario, Note that if you use the RMySQL interface it doesn't matter if the BioMart webservice is available or not. biocLite("RMySQL") mart <- useMart("ensembl","hsapiens_gene_ensembl", mart=TRUE) HTH, Jim Dario Greco wrote: > hi Steffen, > thanks for your help. > now biomart.org is up, but there are still some problems. > > >>mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") > > Error in file(file, "r") : unable to open connection > In addition: Warning message: > unable to resolve 'web50-node4.ebi.ac.uk'. > > and in fact, if i try to open in browser the address > http://www.biomart.org/biomart/martservice > > i get this internal error message: > > > > > OK > The server encountered an internal error or > misconfiguration and was unable to complete > your request. > Please contact the server administrator, > webmaster@mydomain.org and inform them of the time the error > occurred, > and anything you might have done that may have > caused the error. > More information about this error may be available > in the server error log. > > > > what to do? > > thanks again for your kind help > sincerely > Dario > > > > On Tuesday 22 August 2006 15:58, Durinck, Steffen (NIH/NCI) [F] wrote: > >>Hi Dario, >> >>Yes it looks like the website has been down for a few days which explains >>why useMart fails. I've CC'd Arek (BioMart developer) maybe he can shed >>more light on what is happening. >> >>best. >>Steffen >> >> >>-----Original Message----- >>From: Dario Greco [mailto:dario.greco at helsinki.fi] >>Sent: Tue 8/22/2006 4:59 AM >>To: bioconductor at stat.math.ethz.ch >>Subject: [BioC] biomaRt problem >> >>dear list, >>i am trying to annotate some genes using biomaRt, but i am running in the >> >>following problem: >> >>>library(biomaRt) >> >>Loading required package: XML >>Loading required package: RCurl >> >> >>>mart <- useMart("ensembl") >> >>Error in curlPerform(curl = curl, .opts = opts) : >> Couldn't resolve host 'www.biomart.org' >> >>i have also updated to the 1.7.6 version of biomaRt, but no change in the >>result. >> >> >>>sessionInfo() >> >>Version 2.3.1 (2006-06-01) >>i686-redhat-linux-gnu >> >>attached base packages: >>[1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" >>[7] "base" >> >>other attached packages: >> biomaRt RCurl XML >> "1.7.6" "0.6-2" "0.99-8" >> >>i am pretty sure my computer doesn't have any proxy issues. moreover, if i >>try to open the www.biomart.org website in my browser, it appears down. is >>there some problem with the biomart mirror? should i use an alternative >>host? if yes, which? >>do you have any other suggestions? >>thanks in advance for your kind help. >>sincerely >>Dario > > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
ADD REPLYlink written 12.2 years ago by James W. MacDonald48k
Hi Jim, Dario, There is a typo here: mart <- useMart("ensembl","hsapiens_gene_ensembl", mart=TRUE) Should be: mart <- useMart("ensembl","hsapiens_gene_ensembl", mysql=TRUE) Also the EBI BioMart web service is on again. It looks like the BioMart developers shut it down for a while as they where investigating a problem. This is what they mailed me: > there have been problems with people hammering the central server with > martservice requests. We are investigating how to solve this - probably IP > banning I think. > I think the problem below is with the proxy - hopefully I will restart the > server with the correct settings in a few minutes > thanks > Damian This highlights the looping issue: When using the biomaRt package in web service mode we should try not to loop over vectors of identifiers to annotate them but query for the annotation of all these identifiers at once. Alternatively if you can't resist to loop, one should use biomaRt in RMySQL mode. best, Steffen James W. MacDonald wrote: > Hi Dario, Note that if you use the RMySQL interface it doesn't matter > if the BioMart webservice is available or not. biocLite("RMySQL") mart > <- useMart("ensembl","hsapiens_gene_ensembl", mart=TRUE) HTH, Jim > Dario Greco wrote: > hi Steffen, > thanks for your help. > now > biomart.org is up, but there are still some problems. > > >>mart <- > useMart("ensembl", dataset = "hsapiens_gene_ensembl") > > Error in > file(file, "r") : unable to open connection > In addition: Warning > message: > unable to resolve 'web50-node4.ebi.ac.uk'. > > and in fact, > if i try to open in browser the address > > http://www.biomart.org/biomart/martservice > > i get this internal > error message: > > > > > > > > OK > > > The server encountered an internal error or > misconfiguration and > was unable to complete > your request. > > > Please contact the server administrator, > > webmaster@mydomain.org and inform them of the time the error > > occurred, > and anything you might have done that may have > caused > the error. > > > More information about this error may be available > in the server > error log. > > > > > > what to do? > > thanks again for your kind help > sincerely > > Dario > > > > On Tuesday 22 August 2006 15:58, Durinck, Steffen > (NIH/NCI) [F] wrote: > >>Hi Dario, >> >>Yes it looks like the website > has been down for a few days which explains >>why useMart fails. I've > CC'd Arek (BioMart developer) maybe he can shed >>more light on what > is happening. >> >>best. >>Steffen >> >> >>-----Original Message----- > >>From: Dario Greco [mailto:dario.greco at helsinki.fi] >>Sent: Tue > 8/22/2006 4:59 AM >>To: bioconductor at stat.math.ethz.ch >>Subject: > [BioC] biomaRt problem >> >>dear list, >>i am trying to annotate some > genes using biomaRt, but i am running in the >> >>following problem: > >> >>>library(biomaRt) >> >>Loading required package: XML >>Loading > required package: RCurl >> >> >>>mart <- useMart("ensembl") >> >>Error > in curlPerform(curl = curl, .opts = opts) : >> Couldn't resolve host > 'www.biomart.org' >> >>i have also updated to the 1.7.6 version of > biomaRt, but no change in the >>result. >> >> >>>sessionInfo() >> > >>Version 2.3.1 (2006-06-01) >>i686-redhat-linux-gnu >> >>attached > base packages: >>[1] "methods" "stats" "graphics" "grDevices" "utils" > "datasets" >>[7] "base" >> >>other attached packages: >> biomaRt RCurl > XML >> "1.7.6" "0.6-2" "0.99-8" >> >>i am pretty sure my computer > doesn't have any proxy issues. moreover, if i >>try to open the > www.biomart.org website in my browser, it appears down. is >>there > some problem with the biomart mirror? should i use an alternative > >>host? if yes, which? >>do you have any other suggestions? >>thanks > in advance for your kind help. >>sincerely >>Dario > > -- James W. > MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 > CCGC Ann Arbor MI 48109 734-647-5623 > ********************************************************** Electronic > Mail is not secure, may not be read every day, and should not be used > for urgent or sensitive issues. > -- Steffen Durinck, Ph.D. Oncogenomics Section Pediatric Oncology Branch National Cancer Institute, National Institutes of Health URL: http://home.ccr.cancer.gov/oncology/oncogenomics/ Phone: 301-402-8103 Address: Advanced Technology Center, 8717 Grovemont Circle Gaithersburg, MD 20877
ADD REPLYlink written 12.2 years ago by Steffen Durinck580
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