problem connecting to bioMart - NOT proxy error
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Jenny Drnevich ★ 2.0k
@jenny-drnevich-2812
Last seen 17 hours ago
United States
Hi, I've been trying to use biomaRt to connect to BioMart for the last week, and I've been running into a weird problem. I'm not getting any "proxy" errors, so I don't think it's that problem that's mentioned in the vignette and almost all BioC posts on biomaRt connection problems. Here's a quick explanation of the problem, and the code and sessionInfo are below. ensembl = useMart("ensembl") seems to run fine, although it takes 20 seconds or so to get the prompt back. When I put in ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl), R seems to freeze up, or at least the prompt never comes back. I've left it running for 2 hours over lunch one time! This has happened every time I've tried it since last week. I hadn't used biomaRt in about year before then, but I never had this problem before. I don't know if this is related, but I can't get http://www.biomart.org/ to come up on my browser, either, although I have no trouble with http://www.ensembl.org/biomart/martview/. Thanks, Jenny > library(biomaRt) > sessionInfo() R version 2.10.0 (2009-10-26) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.2.0 loaded via a namespace (and not attached): [1] RCurl_1.2-1 XML_2.6-0 > Sys.time() [1] "2009-11-18 16:08:44 CST" > ensembl = useMart("ensembl") > Sys.time() [1] "2009-11-18 16:09:07 CST" > > ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl) ... and then nothing!!! Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at illinois.edu
biomaRt biomaRt • 1.4k views
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 9.6 years ago
Hi Jenny, On 11/18/09 2:25 PM, Jenny Drnevich wrote: > I don't know if this is related, but I > can't get http://www.biomart.org/ to come up on my browser, either, > although I have no trouble with http://www.ensembl.org/biomart/martview/. Hmm, that sounds suspicious. I can browse to that site without problem and seem to be able to connect to both marts quickly (see below). I wonder if you can try connecting from a cafe to try a different network? > library("biomaRt") > system.time(ensembl <- useMart("ensembl")) user system elapsed 0.103 0.006 0.479 > system.time(ensembl <- useDataset("hsapiens_gene_ensembl",mart=ensembl)) Checking attributes ... ok Checking filters ... ok user system elapsed 0.032 0.008 1.902 > sessionInfo() R version 2.11.0 Under development (unstable) (--) i386-apple-darwin10.0.0 locale: [1] en_US.utf-8/en_US.utf-8/C/C/en_US.utf-8/en_US.utf-8 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] biomaRt_2.3.0 loaded via a namespace (and not attached): [1] RCurl_1.2-1 XML_2.6-0
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Hi Seth and James, Thanks for your help. I'm on a desktop, so I don't think I can connect from a different network. The odd thing is that when I started my computer this morning, I was able to get http://www.biomart.org/ up on my browser, pretty quickly. However, then I opened a fresh session of R and had the same problems as before. After that, I wasn't able to get http://www.biomart.org/ again on my browser! I just rebooted my machine, and tried http://www.biomart.org/ on the browser again before starting R; it took several minutes but it finally came up, but then I couldn't get it to re-load (still not having started R). I don't know why I'm having these weird connection problems - maybe my machine is establishing a connection through R, but when it gets hung up it doesn't relinquish the connection even after killing R and rebooting? Time to call in my IT people - any suggestions for things to check out would be appreciated! Thanks, Jenny At 10:08 PM 11/18/2009, Seth Falcon wrote: >Hi Jenny, > >On 11/18/09 2:25 PM, Jenny Drnevich wrote: >>I don't know if this is related, but I >>can't get http://www.biomart.org/ to come up on my browser, either, >>although I have no trouble with http://www.ensembl.org/biomart/martview/. > >Hmm, that sounds suspicious. I can browse to that site without >problem and seem to be able to connect to both marts quickly (see >below). I wonder if you can try connecting from a cafe to try a >different network? > > > > > library("biomaRt") > > system.time(ensembl <- useMart("ensembl")) > user system elapsed > 0.103 0.006 0.479 > > system.time(ensembl <- useDataset("hsapiens_gene_ensembl",mart=ensembl)) >Checking attributes ... ok >Checking filters ... ok > user system elapsed > 0.032 0.008 1.902 > > > sessionInfo() >R version 2.11.0 Under development (unstable) (--) >i386-apple-darwin10.0.0 > >locale: >[1] en_US.utf-8/en_US.utf-8/C/C/en_US.utf-8/en_US.utf-8 > >attached base packages: >[1] stats graphics grDevices datasets utils methods base > >other attached packages: >[1] biomaRt_2.3.0 > >loaded via a namespace (and not attached): >[1] RCurl_1.2-1 XML_2.6-0 Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at illinois.edu
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Hi Jenny, On Thu, Nov 19, 2009 at 8:47 AM, Jenny Drnevich <drnevich at="" illinois.edu=""> wrote: > Thanks for your help. I'm on a desktop, so I don't think I can connect from > a different network. Hey, that's what extension cords are for ;-) > The odd thing is that when I started my computer this > morning, I was able to get http://www.biomart.org/ up on my browser, pretty > quickly. However, then I opened a fresh session of R and had the same > problems as before. After that, I wasn't able to get http://www.biomart.org/ > again on my browser! I just rebooted my machine, and tried > http://www.biomart.org/ on the browser again before starting R; it took > several minutes but it finally came up, but then I couldn't get it to > re-load (still not having started R). ?I don't know why I'm having these > weird connection problems - maybe my machine is establishing a connection > through R, but when it gets hung up it doesn't relinquish the connection > even after killing R and rebooting? Time to call in my IT people - any > suggestions for things to check out would be appreciated! One thing to be aware of is that I believe the biomart site imposes some rate limits and possibly temporary blocks when it receives too many requests in a short period of time. I'm not up on the details so might be getting this wrong. If they are indeed doing some dynamic blocking/limiting based on query rate, then a misbehaving colleague could impact your access. Otherwise, it would be worth asking for some local IT support to assess general network connectivity to the biomart server. For example, if you get a lot of packet loss when pinging their server, that might give you an idea that the problem is at a more generic networking level. + seth > > Thanks, > Jenny > > At 10:08 PM 11/18/2009, Seth Falcon wrote: >> >> Hi Jenny, >> >> On 11/18/09 2:25 PM, Jenny Drnevich wrote: >>> >>> I don't know if this is related, but I >>> can't get http://www.biomart.org/ to come up on my browser, either, >>> although I have no trouble with http://www.ensembl.org/biomart/martview/. >> >> Hmm, that sounds suspicious. ?I can browse to that site without problem >> and seem to be able to connect to both marts quickly (see below). ?I wonder >> if you can try connecting from a cafe to try a different network? >> >> >> >> > library("biomaRt") >> > system.time(ensembl <- useMart("ensembl")) >> ? user ?system elapsed >> ?0.103 ? 0.006 ? 0.479 >> > ?system.time(ensembl <- >> > useDataset("hsapiens_gene_ensembl",mart=ensembl)) >> Checking attributes ... ok >> Checking filters ... ok >> ? user ?system elapsed >> ?0.032 ? 0.008 ? 1.902 >> >> > sessionInfo() >> R version 2.11.0 Under development (unstable) (--) >> i386-apple-darwin10.0.0 >> >> locale: >> [1] en_US.utf-8/en_US.utf-8/C/C/en_US.utf-8/en_US.utf-8 >> >> attached base packages: >> [1] stats ? ? graphics ?grDevices datasets ?utils ? ? methods ? base >> >> other attached packages: >> [1] biomaRt_2.3.0 >> >> loaded via a namespace (and not attached): >> [1] RCurl_1.2-1 XML_2.6-0 > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at illinois.edu > > _______________________________________________ > 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 > -- Seth Falcon | @sfalcon | http://userprimary.net/user
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James F. Reid ▴ 610
@james-f-reid-3148
Last seen 9.6 years ago
Hi Jenny, I don't see this on my side and I have the set-up as you so I guess it must some connection issue. I can also open the web page http://www.biomart.org/. Can you confirm that this is happening in a 'fresh' session i.e. with not many previous open connections? Best, James. Here is my session: > library(biomaRt) > sessionInfo() R version 2.10.0 (2009-10-26) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.2.0 loaded via a namespace (and not attached): [1] RCurl_1.2-1 XML_2.6-0 > ensembl = useMart("ensembl") > ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl) Checking attributes ... ok Checking filters ... ok > Jenny Drnevich wrote: > Hi, > > I've been trying to use biomaRt to connect to BioMart for the last week, > and I've been running into a weird problem. I'm not getting any "proxy" > errors, so I don't think it's that problem that's mentioned in the > vignette and almost all BioC posts on biomaRt connection problems. > Here's a quick explanation of the problem, and the code and sessionInfo > are below. ensembl = useMart("ensembl") seems to run fine, although it > takes 20 seconds or so to get the prompt back. When I put in ensembl = > useDataset("hsapiens_gene_ensembl",mart=ensembl), R seems to freeze up, > or at least the prompt never comes back. I've left it running for 2 > hours over lunch one time! This has happened every time I've tried it > since last week. I hadn't used biomaRt in about year before then, but I > never had this problem before. I don't know if this is related, but I > can't get http://www.biomart.org/ to come up on my browser, either, > although I have no trouble with http://www.ensembl.org/biomart/martview/. > > Thanks, > Jenny > > > > library(biomaRt) > > sessionInfo() > R version 2.10.0 (2009-10-26) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.2.0 > > loaded via a namespace (and not attached): > [1] RCurl_1.2-1 XML_2.6-0 > > Sys.time() > [1] "2009-11-18 16:08:44 CST" > > ensembl = useMart("ensembl") > > Sys.time() > [1] "2009-11-18 16:09:07 CST" > > > > ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl) > > ... and then nothing!!! > > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at illinois.edu > > _______________________________________________ > 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 >
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