biomaaRt error: Extra content at the end of the document
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Hari Easwaran ▴ 240
@hari-easwaran-3510
Last seen 6.4 years ago
United States
Hi all, I am facing a problem with biomaRT which was working fine until yesterday. This is what I ma doing: library(biomaRt) library(RCurl) ensembl54 = useMart(host="may2009.archive.ensembl.org", biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl") #Get the hg18 version in biomart I am getting the following error: Extra content at the end of the document Error: 1: Extra content at the end of the document I started facing this issue only today. Any idea what could be wrong and if there isa way to fix it. Appreciate any help or suggestions. Here's my session info: > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.12.0 RCurl_1.95-4.1 bitops_1.0-6 [4] biomaRt_2.18.0 loaded via a namespace (and not attached): [1] tools_3.0.2 XML_3.95-0.2 Sincerely Hari Easwaran Johns Hopkins University Baltimore, MD 21117 [[alternative HTML version deleted]]
biomaRt biomaRt • 2.8k views
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@steffen-durinck-4465
Last seen 7.1 years ago
Hi Hari, If you go to the web page of BioMart for that specific archive you'll see that is temporarily unavailable. http://may2009.archive.ensembl.org/biomart/martview I would check again in a bit and if this site comes back, you should be able to do your queries with biomaRt again. If it is out too long, contact the ensembl helpdesk at helpdesk@ensembl.organd report this issue so it can be fixed. Cheers, Steffen On Thu, Jan 16, 2014 at 9:21 AM, Hari Easwaran <hariharan.pe@gmail.com>wrote: > Hi all, > I am facing a problem with biomaRT which was working fine until yesterday. > This is what I ma doing: > library(biomaRt) > library(RCurl) > ensembl54 = useMart(host="may2009.archive.ensembl.org", > biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl") #Get the > hg18 version in biomart > > I am getting the following error: > Extra content at the end of the document > Error: 1: Extra content at the end of the document > > I started facing this issue only today. Any idea what could be wrong and > if there isa way to fix it. Appreciate any help or suggestions. > > Here's my session info: > > sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.12.0 RCurl_1.95-4.1 bitops_1.0-6 > [4] biomaRt_2.18.0 > > loaded via a namespace (and not attached): > [1] tools_3.0.2 XML_3.95-0.2 > > > Sincerely > Hari Easwaran > Johns Hopkins University > Baltimore, MD 21117 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Hi Steffen, Thanks for your help. Sincerely, Hari On Thu, Jan 16, 2014 at 12:38 PM, Steffen Durinck <durinck.steffen@gene.com>wrote: > Hi Hari, > > If you go to the web page of BioMart for that specific archive you'll see > that is temporarily unavailable. > > http://may2009.archive.ensembl.org/biomart/martview > > I would check again in a bit and if this site comes back, you should be > able to do your queries with biomaRt again. > > If it is out too long, contact the ensembl helpdesk at > helpdesk@ensembl.org and report this issue so it can be fixed. > > Cheers, > Steffen > > > > > On Thu, Jan 16, 2014 at 9:21 AM, Hari Easwaran <hariharan.pe@gmail.com>wrote: > >> Hi all, >> I am facing a problem with biomaRT which was working fine until yesterday. >> This is what I ma doing: >> library(biomaRt) >> library(RCurl) >> ensembl54 = useMart(host="may2009.archive.ensembl.org", >> biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl") #Get the >> hg18 version in biomart >> >> I am getting the following error: >> Extra content at the end of the document >> Error: 1: Extra content at the end of the document >> >> I started facing this issue only today. Any idea what could be wrong and >> if there isa way to fix it. Appreciate any help or suggestions. >> >> Here's my session info: >> > sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] BiocInstaller_1.12.0 RCurl_1.95-4.1 bitops_1.0-6 >> [4] biomaRt_2.18.0 >> >> loaded via a namespace (and not attached): >> [1] tools_3.0.2 XML_3.95-0.2 >> >> >> Sincerely >> Hari Easwaran >> Johns Hopkins University >> Baltimore, MD 21117 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]
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